Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/0501_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/0501_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/0501_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/0501_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0501_R1.fq.gz Writing a C -> T converted version of the input file 0501_R1.fq.gz to 0501_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0501_R1.fq.gz to 0501_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0501_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0501_R2.fq.gz Writing a C -> T converted version of the input file 0501_R2.fq.gz to 0501_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0501_R2.fq.gz to 0501_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0501_R2.fq.gz (100001 sequences in total) Input files are 0501_R1.fq.gz_C_to_T.fastq and 0501_R1.fq.gz_G_to_A.fastq and 0501_R2.fq.gz_C_to_T.fastq and 0501_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 0501_R1.fq.gz_C_to_T.fastq and 0501_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:3407:1309_1:N:0:NGATGT/1 99 NC_047560.1_CT_converted 16721315 8 140M = 16721391 215 GTATATTGAATATGAGATATATTTGTATATATATTGTAAGTTTGTAAAAATGTTTAAAAATTTTATATTAATTTAATATTGTTTTATATATAGTTTATAGATTTATATGGATTATGGTATTTTTTTGAATTTTGATTATT FJJJJJJJFAF>> Writing bisulfite mapping results to 0501_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/0501_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/0501_R2.fq.gz 100000 reads; of these: 100000 (100.00%100000) were paired; of these: reads; of these: 99538100000 ( (99.54%) aligned concordantly 0 times 291 (100.000.29%%) were paired; of these:) aligned concordantly exactly 1 time 99565171 ( (99.560.17%%) aligned concordantly 0 times) aligned concordantly >1 times 0.46262% ( overall alignment rate0.26 %) aligned concordantly exactly 1 time 173 (0.17%) aligned concordantly >1 times 0.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 53128 (53.13%) aligned concordantly 0 times 21978 (21.98%) aligned concordantly exactly 1 time 24894 (10000024.89 reads; of these:% ) aligned concordantly >1 times 10000046.87 (% overall alignment rate 100.00%) were paired; of these: 53054 (53.05%) aligned concordantly 0 times 22096 (22.10%) aligned concordantly exactly 1 time 24850 (24.85%) aligned concordantly >1 times 46.95% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 0501_R1.fq.gz_C_to_T.fastq, 0501_R1.fq.gz_G_to_A.fastq, 0501_R2.fq.gz_C_to_T.fastq and 0501_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 59640 Mapping efficiency: 59.6% Sequence pairs with no alignments under any condition: 30009 Sequence pairs did not map uniquely: 10351 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 29836 ((converted) top strand) GA/CT/CT: 13 (complementary to (converted) top strand) GA/CT/GA: 14 (complementary to (converted) bottom strand) CT/GA/GA: 29777 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2510127 Total methylated C's in CpG context: 39770 Total methylated C's in CHG context: 3532 Total methylated C's in CHH context: 16591 Total methylated C's in Unknown context: 262 Total unmethylated C's in CpG context: 262307 Total unmethylated C's in CHG context: 406581 Total unmethylated C's in CHH context: 1781346 Total unmethylated C's in Unknown context: 7688 C methylated in CpG context: 13.2% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 3.3% Bismark completed in 0d 0h 0m 56s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/0502_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/0502_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/0502_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/0502_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0502_R1.fq.gz Writing a C -> T converted version of the input file 0502_R1.fq.gz to 0502_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0502_R1.fq.gz to 0502_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0502_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0502_R2.fq.gz Writing a C -> T converted version of the input file 0502_R2.fq.gz to 0502_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0502_R2.fq.gz to 0502_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0502_R2.fq.gz (100001 sequences in total) Input files are 0502_R1.fq.gz_C_to_T.fastq and 0502_R1.fq.gz_G_to_A.fastq and 0502_R2.fq.gz_C_to_T.fastq and 0502_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 0502_R1.fq.gz_C_to_T.fastq and 0502_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:4949:1309_1:N:0:NAGATC/1 99 NC_047563.1_CT_converted 48458015 0 140M = 48458040 165 AATTTTTTTTAATTTAGTATATTAATATTTTAATTTTATATTTTAATGAAATTATGTTTTATAAGTGAGAGGAAAAAATTGTATAAAAGATTAGAGTTTAGTTGATGGGTTTTTAAAATTGTTGGATTAAGTTATGTTTT A-JJJJJFJJ<-FJJ---FJJJJFJFJ-FJJJ>> Writing bisulfite mapping results to 0502_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/0502_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/0502_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99664 (99.66%) aligned concordantly 0 times 220 (0.22%) aligned concordantly exactly 1 time 116 (0.12%) aligned concordantly >1 times 0.34% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99687 (99.69%) aligned concordantly 0 times 209 (0.21%) aligned concordantly exactly 1 time 104 (0.10%) aligned concordantly >1 times 0.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 53540 (53.54%) aligned concordantly 0 times 22119 (22.12%) aligned concordantly exactly 1 time 24341 (24.34%) aligned concordantly >1 times 46.46% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 53801 (53.80%) aligned concordantly 0 times 21982 (21.98%) aligned concordantly exactly 1 time 24217 (24.22%) aligned concordantly >1 times 46.20% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 0502_R1.fq.gz_C_to_T.fastq, 0502_R1.fq.gz_G_to_A.fastq, 0502_R2.fq.gz_C_to_T.fastq and 0502_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 59284 Mapping efficiency: 59.3% Sequence pairs with no alignments under any condition: 30449 Sequence pairs did not map uniquely: 10267 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 29531 ((converted) top strand) GA/CT/CT: 8 (complementary to (converted) top strand) GA/CT/GA: 2 (complementary to (converted) bottom strand) CT/GA/GA: 29743 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2538444 Total methylated C's in CpG context: 39048 Total methylated C's in CHG context: 4019 Total methylated C's in CHH context: 17093 Total methylated C's in Unknown context: 324 Total unmethylated C's in CpG context: 261599 Total unmethylated C's in CHG context: 413167 Total unmethylated C's in CHH context: 1803518 Total unmethylated C's in Unknown context: 7724 C methylated in CpG context: 13.0% C methylated in CHG context: 1.0% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 4.0% Bismark completed in 0d 0h 0m 55s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/0503_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/0503_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/0503_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/0503_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0503_R1.fq.gz Writing a C -> T converted version of the input file 0503_R1.fq.gz to 0503_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0503_R1.fq.gz to 0503_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0503_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/0503_R2.fq.gz Writing a C -> T converted version of the input file 0503_R2.fq.gz to 0503_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 0503_R2.fq.gz to 0503_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 0503_R2.fq.gz (100001 sequences in total) Input files are 0503_R1.fq.gz_C_to_T.fastq and 0503_R1.fq.gz_G_to_A.fastq and 0503_R2.fq.gz_C_to_T.fastq and 0503_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 0503_R1.fq.gz_C_to_T.fastq and 0503_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:5578:1309_1:N:0:NTGTCA/1 77 * 0 0 * * 0 0 GTTTTGAGGTTTTTTTTGTTTTGAATAAAATTTGGTTTTTTATTTTGTAATTTATATTTATTTTTTTATAAGGATGATTTGTGTTAAATTTGGTTTAATTTAGTTAAGTGGTTTTAGAGAAAATGATTATAATGTAAAAA JJJJJJJJJJJJJJJJJFJJJJAJJJJ-7->> Writing bisulfite mapping results to 0503_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/0503_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/0503_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99574 (99.57%) aligned concordantly 0 times 266 (0.27%) aligned concordantly exactly 1 time 160 (0.16%) aligned concordantly >1 times 0.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 53600 (53.60%) aligned concordantly 0 times 22022 (22.02%) aligned concordantly exactly 1 time 24378 (24.38%) aligned concordantly >1 times 46.40% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99574 (99.57%) aligned concordantly 0 times 274 (0.27%) aligned concordantly exactly 1 time 152 (0.15%) aligned concordantly >1 times 0.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 53574 (53.57%) aligned concordantly 0 times 22090 (22.09%) aligned concordantly exactly 1 time 24336 (24.34%) aligned concordantly >1 times 46.43% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 0503_R1.fq.gz_C_to_T.fastq, 0503_R1.fq.gz_G_to_A.fastq, 0503_R2.fq.gz_C_to_T.fastq and 0503_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 59416 Mapping efficiency: 59.4% Sequence pairs with no alignments under any condition: 30587 Sequence pairs did not map uniquely: 9997 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 29711 ((converted) top strand) GA/CT/CT: 9 (complementary to (converted) top strand) GA/CT/GA: 20 (complementary to (converted) bottom strand) CT/GA/GA: 29676 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2464248 Total methylated C's in CpG context: 40925 Total methylated C's in CHG context: 3621 Total methylated C's in CHH context: 17614 Total methylated C's in Unknown context: 284 Total unmethylated C's in CpG context: 249148 Total unmethylated C's in CHG context: 395141 Total unmethylated C's in CHH context: 1757799 Total unmethylated C's in Unknown context: 7377 C methylated in CpG context: 14.1% C methylated in CHG context: 0.9% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.7% Bismark completed in 0d 0h 0m 54s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/3501_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/3501_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/3501_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/3501_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3501_R1.fq.gz Writing a C -> T converted version of the input file 3501_R1.fq.gz to 3501_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3501_R1.fq.gz to 3501_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3501_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3501_R2.fq.gz Writing a C -> T converted version of the input file 3501_R2.fq.gz to 3501_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3501_R2.fq.gz to 3501_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3501_R2.fq.gz (100001 sequences in total) Input files are 3501_R1.fq.gz_C_to_T.fastq and 3501_R1.fq.gz_G_to_A.fastq and 3501_R2.fq.gz_C_to_T.fastq and 3501_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 3501_R1.fq.gz_C_to_T.fastq and 3501_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:9394:1309_1:N:0:NGACCA/1 77 * 0 0 * * 0 0 TAGGGTAAATATATATATAGATTTAATGTATTGGTTTGTTTATTTTATTTAAATGAGTTTGAATGTAAAGTTATTAGATTTTGGATTTTTATTATTATAGTTTTTTGGAAAGGAAAATTTTATTTGTAAAGGTAATTATG JJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJJ7FJJJJJJJJJJJJJJAJJJJJJJJFJJJJJJFJJJJFJAJFJAFAF<>> Writing bisulfite mapping results to 3501_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/3501_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/3501_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99604 (99.60%) aligned concordantly 0 times 265 (0.27%) aligned concordantly exactly 1 time 131 (0.13%) aligned concordantly >1 times 0.40% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99617 (99.62%) aligned concordantly 0 times 258 (0.26%) aligned concordantly exactly 1 time 125 (0.12%) aligned concordantly >1 times 0.38% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 51982 (51.98%) aligned concordantly 0 times 22559 (22.56%) aligned concordantly exactly 1 time 25459 (25.46%) aligned concordantly >1 times 48.02% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 52235 (52.23%) aligned concordantly 0 times 22425 (22.43%) aligned concordantly exactly 1 time 25340 (25.34%) aligned concordantly >1 times 47.77% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 3501_R1.fq.gz_C_to_T.fastq, 3501_R1.fq.gz_G_to_A.fastq, 3501_R2.fq.gz_C_to_T.fastq and 3501_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60904 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 28435 Sequence pairs did not map uniquely: 10661 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30342 ((converted) top strand) GA/CT/CT: 7 (complementary to (converted) top strand) GA/CT/GA: 11 (complementary to (converted) bottom strand) CT/GA/GA: 30544 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2586683 Total methylated C's in CpG context: 38139 Total methylated C's in CHG context: 3842 Total methylated C's in CHH context: 16449 Total methylated C's in Unknown context: 294 Total unmethylated C's in CpG context: 269842 Total unmethylated C's in CHG context: 414374 Total unmethylated C's in CHH context: 1844037 Total unmethylated C's in Unknown context: 7767 C methylated in CpG context: 12.4% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 3.6% Bismark completed in 0d 0h 0m 57s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/3502_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/3502_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/3502_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/3502_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3502_R1.fq.gz Writing a C -> T converted version of the input file 3502_R1.fq.gz to 3502_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3502_R1.fq.gz to 3502_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3502_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3502_R2.fq.gz Writing a C -> T converted version of the input file 3502_R2.fq.gz to 3502_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3502_R2.fq.gz to 3502_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3502_R2.fq.gz (100001 sequences in total) Input files are 3502_R1.fq.gz_C_to_T.fastq and 3502_R1.fq.gz_G_to_A.fastq and 3502_R2.fq.gz_C_to_T.fastq and 3502_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 3502_R1.fq.gz_C_to_T.fastq and 3502_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:3325:1309_1:N:0:NTTGTA/1 77 * 0 0 * * 0 0 AAAGAATAATGGAAGATAGGTTGTGTTTGATTTTAAAATTTTGTTAGTAATGTTTGTTTTTTAAAAGATAATTTTATGAGATGGATTGAAATTTATTTATTTTTATTATTTTATAATTAATTAGGAATTTGTATAAATTA A>> Writing bisulfite mapping results to 3502_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/3502_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/3502_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99660 (99.66%) aligned concordantly 0 times 215 (0.21%) aligned concordantly exactly 1 time 125 (0.12%) aligned concordantly >1 times 0.34% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99671 (99.67%) aligned concordantly 0 times 207 (0.21%) aligned concordantly exactly 1 time 122 (0.12%) aligned concordantly >1 times 0.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 52098 (52.10%) aligned concordantly 0 times 22743 (22.74%) aligned concordantly exactly 1 time 25159 (25.16%) aligned concordantly >1 times 47.90% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 52188 (52.19%) aligned concordantly 0 times 22743 (22.74%) aligned concordantly exactly 1 time 25069 (25.07%) aligned concordantly >1 times 47.81% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 3502_R1.fq.gz_C_to_T.fastq, 3502_R1.fq.gz_G_to_A.fastq, 3502_R2.fq.gz_C_to_T.fastq and 3502_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61008 Mapping efficiency: 61.0% Sequence pairs with no alignments under any condition: 28396 Sequence pairs did not map uniquely: 10596 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30455 ((converted) top strand) GA/CT/CT: 5 (complementary to (converted) top strand) GA/CT/GA: 9 (complementary to (converted) bottom strand) CT/GA/GA: 30539 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2617130 Total methylated C's in CpG context: 38787 Total methylated C's in CHG context: 3814 Total methylated C's in CHH context: 16132 Total methylated C's in Unknown context: 318 Total unmethylated C's in CpG context: 272956 Total unmethylated C's in CHG context: 424987 Total unmethylated C's in CHH context: 1860454 Total unmethylated C's in Unknown context: 7826 C methylated in CpG context: 12.4% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 3.9% Bismark completed in 0d 0h 0m 57s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/3503_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/3503_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/3503_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/3503_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3503_R1.fq.gz Writing a C -> T converted version of the input file 3503_R1.fq.gz to 3503_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3503_R1.fq.gz to 3503_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3503_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/3503_R2.fq.gz Writing a C -> T converted version of the input file 3503_R2.fq.gz to 3503_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 3503_R2.fq.gz to 3503_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 3503_R2.fq.gz (100001 sequences in total) Input files are 3503_R1.fq.gz_C_to_T.fastq and 3503_R1.fq.gz_G_to_A.fastq and 3503_R2.fq.gz_C_to_T.fastq and 3503_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 3503_R1.fq.gz_C_to_T.fastq and 3503_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:6512:1309_1:N:0:NCGTCC/1 99 NC_047563.1_CT_converted 30894107 2 140M = 30894317 350 ATAATATATATTATAGTATAGTATAGTATTGAAATTTTATAGTATAGTATTGAAATTTTATAGTATAGTATTGGAATTTTATATTATAGTATATAATTTTTTAGAATTGTTTTTATTATATTATATTATAGTATATTATA JJFJF>> Writing bisulfite mapping results to 3503_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/3503_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/3503_R2.fq.gz 100000 reads; of these: 100000 (100000 reads; of these: 100.00 %100000) were paired; of these: ( 99682 (99.68100.00%%) aligned concordantly 0 times) were paired; of these: 20899677 ( (0.2199.68%%) aligned concordantly exactly 1 time) aligned concordantly 0 times 110198 ( (0.110.20%%) aligned concordantly >1 times) aligned concordantly exactly 1 time 0.32 %125 overall alignment rate ( 0.12%) aligned concordantly >1 times 0.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 55137 (55.14%) aligned concordantly 0 times 21128 (21.13%) aligned concordantly exactly 1 time 23735 (23.73%) aligned concordantly >1 times 44.86% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 54970 (54.97%) aligned concordantly 0 times 21374 (21.37%) aligned concordantly exactly 1 time 23656 (23.66%) aligned concordantly >1 times 45.03% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 3503_R1.fq.gz_C_to_T.fastq, 3503_R1.fq.gz_G_to_A.fastq, 3503_R2.fq.gz_C_to_T.fastq and 3503_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 57332 Mapping efficiency: 57.3% Sequence pairs with no alignments under any condition: 32794 Sequence pairs did not map uniquely: 9874 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 28576 ((converted) top strand) GA/CT/CT: 6 (complementary to (converted) top strand) GA/CT/GA: 8 (complementary to (converted) bottom strand) CT/GA/GA: 28742 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2445297 Total methylated C's in CpG context: 38255 Total methylated C's in CHG context: 3452 Total methylated C's in CHH context: 15550 Total methylated C's in Unknown context: 243 Total unmethylated C's in CpG context: 252250 Total unmethylated C's in CHG context: 395300 Total unmethylated C's in CHH context: 1740490 Total unmethylated C's in Unknown context: 7083 C methylated in CpG context: 13.2% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 3.3% Bismark completed in 0d 0h 0m 55s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/5201_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/5201_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/5201_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5201_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5201_R1.fq.gz Writing a C -> T converted version of the input file 5201_R1.fq.gz to 5201_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5201_R1.fq.gz to 5201_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5201_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5201_R2.fq.gz Writing a C -> T converted version of the input file 5201_R2.fq.gz to 5201_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5201_R2.fq.gz to 5201_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5201_R2.fq.gz (100001 sequences in total) Input files are 5201_R1.fq.gz_C_to_T.fastq and 5201_R1.fq.gz_G_to_A.fastq and 5201_R2.fq.gz_C_to_T.fastq and 5201_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 5201_R1.fq.gz_C_to_T.fastq and 5201_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:4787:1309_1:N:0:NCAGTG/1 77 * 0 0 * * 0 0 TAAAGTTTAGATAATTTTTATATTGGGTTGTTTGATATGTTAAAATTTTAGTTTAATTTTATGGAAAATATTTAAATTTATTTTTGTTTGTTTTGAAATTTTATGATTTTAAAATATTTTGATATATAATATGTATATAT JJFAJFJJFAJJJJFFAJJFF7FF7FF-FA>> Writing bisulfite mapping results to 5201_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5201_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5201_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99505 (99.50%) aligned concordantly 0 times 337 (0.34%100000) aligned concordantly exactly 1 time reads; of these: 158100000 ( (0.16%) aligned concordantly >1 times 1000000.49100.00 reads; of these:%% overall alignment rate) were paired; of these: 100000 (52496 (52.50%) aligned concordantly 0 times100.00 % ) were paired; of these:22432 ( 22.4352380% () aligned concordantly exactly 1 time52.38 % ) aligned concordantly 0 times25072 ( 25.0722756% () aligned concordantly >1 times22.76 %47.50) aligned concordantly exactly 1 time% overall alignment rate 10000024864 reads; of these: ( 24.86 %100000) aligned concordantly >1 times ( 47.62% overall alignment rate 100.00%) were paired; of these: 99467 (99.47%) aligned concordantly 0 times 369 (0.37%) aligned concordantly exactly 1 time 164 (0.16%) aligned concordantly >1 times 0.53% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5201_R1.fq.gz_C_to_T.fastq, 5201_R1.fq.gz_G_to_A.fastq, 5201_R2.fq.gz_C_to_T.fastq and 5201_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60895 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 28803 Sequence pairs did not map uniquely: 10302 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30438 ((converted) top strand) GA/CT/CT: 11 (complementary to (converted) top strand) GA/CT/GA: 7 (complementary to (converted) bottom strand) CT/GA/GA: 30439 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2482069 Total methylated C's in CpG context: 35234 Total methylated C's in CHG context: 2928 Total methylated C's in CHH context: 13361 Total methylated C's in Unknown context: 286 Total unmethylated C's in CpG context: 254332 Total unmethylated C's in CHG context: 390650 Total unmethylated C's in CHH context: 1785564 Total unmethylated C's in Unknown context: 7876 C methylated in CpG context: 12.2% C methylated in CHG context: 0.7% C methylated in CHH context: 0.7% C methylated in unknown context (CN or CHN): 3.5% Bismark completed in 0d 0h 0m 55s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/5202_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/5202_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/5202_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5202_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5202_R1.fq.gz Writing a C -> T converted version of the input file 5202_R1.fq.gz to 5202_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5202_R1.fq.gz to 5202_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5202_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5202_R2.fq.gz Writing a C -> T converted version of the input file 5202_R2.fq.gz to 5202_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5202_R2.fq.gz to 5202_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5202_R2.fq.gz (100001 sequences in total) Input files are 5202_R1.fq.gz_C_to_T.fastq and 5202_R1.fq.gz_G_to_A.fastq and 5202_R2.fq.gz_C_to_T.fastq and 5202_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 5202_R1.fq.gz_C_to_T.fastq and 5202_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:5964:1309_1:N:0:NGTCAA/1 99 NC_047560.1_CT_converted 37503292 1 140M = 37503332 180 GGATATAGATTGAGTGGTATATATATGTAGTTAAGGTAATTAAGAATGATTTTAATAAAATATTTTGTTGAGTAATGTAAGTTTTTAAGAAAGTAATATTTATATTTGTTTAAAATATAATATTTAAATATTTTGTTTTA JJFJ>> Writing bisulfite mapping results to 5202_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5202_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5202_R2.fq.gz Chromosomal sequence could not be extracted for GWNJ-0901:413:GW1904042006th:6:1101:22059:9536_1:N:0:AGTCAA NC_001276.1 1 100000 reads; of these: 100000 (100.00%) were paired; of these: 99705 (99.70%) aligned concordantly 0 times 197 (0.20%) aligned concordantly exactly 1 time 98 (0.10%) aligned concordantly >1 times 0.29% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99685 (99.69%) aligned concordantly 0 times 210 (0.21%) aligned concordantly exactly 1 time 105 (0.10%) aligned concordantly >1 times 0.32% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 52173 (52.17%) aligned concordantly 0 times 22633 (22.63%) aligned concordantly exactly 1 time 25194 (25.19%) aligned concordantly >1 times 47.83% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 52546 (52.55%) aligned concordantly 0 times 22443 (22.44%) aligned concordantly exactly 1 time 25011 (25.01%) aligned concordantly >1 times 47.45% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5202_R1.fq.gz_C_to_T.fastq, 5202_R1.fq.gz_G_to_A.fastq, 5202_R2.fq.gz_C_to_T.fastq and 5202_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60900 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 28595 Sequence pairs did not map uniquely: 10505 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30633 ((converted) top strand) GA/CT/CT: 6 (complementary to (converted) top strand) GA/CT/GA: 6 (complementary to (converted) bottom strand) CT/GA/GA: 30254 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2645668 Total methylated C's in CpG context: 37073 Total methylated C's in CHG context: 3678 Total methylated C's in CHH context: 15876 Total methylated C's in Unknown context: 262 Total unmethylated C's in CpG context: 282623 Total unmethylated C's in CHG context: 432596 Total unmethylated C's in CHH context: 1873822 Total unmethylated C's in Unknown context: 7796 C methylated in CpG context: 11.6% C methylated in CHG context: 0.8% C methylated in CHH context: 0.8% C methylated in unknown context (CN or CHN): 3.3% Bismark completed in 0d 0h 0m 56s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/5203_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/5203_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/5203_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5203_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5203_R1.fq.gz Writing a C -> T converted version of the input file 5203_R1.fq.gz to 5203_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5203_R1.fq.gz to 5203_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5203_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5203_R2.fq.gz Writing a C -> T converted version of the input file 5203_R2.fq.gz to 5203_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5203_R2.fq.gz to 5203_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5203_R2.fq.gz (100001 sequences in total) Input files are 5203_R1.fq.gz_C_to_T.fastq and 5203_R1.fq.gz_G_to_A.fastq and 5203_R2.fq.gz_C_to_T.fastq and 5203_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 5203_R1.fq.gz_C_to_T.fastq and 5203_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:11028:2100_1:N:0:GTCCGC/1 99 NC_047568.1_CT_converted 12344861 42 140M = 12344910 189 AATAAATATAATAATAGAATTATGAGATTTTTTTTTTTTAAAGTTATTGATGATTAATTTAATAAGTGATATATAAATTATAGGAATTGAAGGATAATAAATTTTATTATTAGATATTTAGATGATAAAATGTAATTTGA AFJJFFJJJJJFFJAFAFJJJJAJ-<--F7FJJJJJJJJJJFF7F-FAAJAJFJJ-FJJJ-AFFJFJAFJJJJJFJJJJ>> Writing bisulfite mapping results to 5203_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5203_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5203_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 54159 (54.16%) aligned concordantly 0 times 21345 (21.34%) aligned concordantly exactly 1 time 24496 (24.50%) aligned concordantly >1 times 45.84% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99574 (99.57%) aligned concordantly 0 times 250 (0.25%) aligned concordantly exactly 1 time 176 (0.18%) aligned concordantly >1 times 0.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99599 (99.60%) aligned concordantly 0 times 245 (0.24%) aligned concordantly exactly 1 time 156 (0.16%) aligned concordantly >1 times 0.40% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 54059 (54.06%) aligned concordantly 0 times 21314 (21.31%) aligned concordantly exactly 1 time 24627 (24.63%) aligned concordantly >1 times 45.94% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5203_R1.fq.gz_C_to_T.fastq, 5203_R1.fq.gz_G_to_A.fastq, 5203_R2.fq.gz_C_to_T.fastq and 5203_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 58371 Mapping efficiency: 58.4% Sequence pairs with no alignments under any condition: 31612 Sequence pairs did not map uniquely: 10017 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 29260 ((converted) top strand) GA/CT/CT: 14 (complementary to (converted) top strand) GA/CT/GA: 17 (complementary to (converted) bottom strand) CT/GA/GA: 29080 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2443828 Total methylated C's in CpG context: 39076 Total methylated C's in CHG context: 3876 Total methylated C's in CHH context: 17506 Total methylated C's in Unknown context: 272 Total unmethylated C's in CpG context: 251416 Total unmethylated C's in CHG context: 392308 Total unmethylated C's in CHH context: 1739646 Total unmethylated C's in Unknown context: 7294 C methylated in CpG context: 13.5% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% C methylated in unknown context (CN or CHN): 3.6% Bismark completed in 0d 0h 0m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/5901_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/5901_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/5901_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5901_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5901_R1.fq.gz Writing a C -> T converted version of the input file 5901_R1.fq.gz to 5901_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5901_R1.fq.gz to 5901_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5901_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5901_R2.fq.gz Writing a C -> T converted version of the input file 5901_R2.fq.gz to 5901_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5901_R2.fq.gz to 5901_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5901_R2.fq.gz (100001 sequences in total) Input files are 5901_R1.fq.gz_C_to_T.fastq and 5901_R1.fq.gz_G_to_A.fastq and 5901_R2.fq.gz_C_to_T.fastq and 5901_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 5901_R1.fq.gz_C_to_T.fastq and 5901_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:5802:1309_1:N:0:NCCAAT/1 77 * 0 0 * * 0 0 AATATTAAAATATATTTATATATGATATTATGTATTTTAATTTTTTTTTTGTAAATAATAGATTTTTTTATAAAGTTGTATAAATTTATTAAAAATTTAATAAATGATTGTAAAATTAAGTATAGTATTTTTTATTAATA FAJFJFJFFFJJJJJJJFJ>> Writing bisulfite mapping results to 5901_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5901_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5901_R2.fq.gz 100000 reads; of these: 100000100000 reads; of these: ( 100000 (100.00%) were paired; of these: 100.0053410% () were paired; of these:53.41 % ) aligned concordantly 0 times99638 ( 99.6422176% () aligned concordantly 0 times22.18 % ) aligned concordantly exactly 1 time238 ( 0.2424414% () aligned concordantly exactly 1 time24.41 % ) aligned concordantly >1 times124100000 ( reads; of these:46.590.12 %% overall alignment rate) aligned concordantly >1 times100000 (0.36% overall alignment rate 100.00%) were paired; of these: 99640 (99.64%) aligned concordantly 0 times 235 (0.23%) aligned concordantly exactly 1 time 125 (0.12%) aligned concordantly >1 times 0.36% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 53182 (53.18%) aligned concordantly 0 times 22257 (22.26%) aligned concordantly exactly 1 time 24561 (24.56%) aligned concordantly >1 times 46.82% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5901_R1.fq.gz_C_to_T.fastq, 5901_R1.fq.gz_G_to_A.fastq, 5901_R2.fq.gz_C_to_T.fastq and 5901_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 59788 Mapping efficiency: 59.8% Sequence pairs with no alignments under any condition: 29986 Sequence pairs did not map uniquely: 10226 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 29983 ((converted) top strand) GA/CT/CT: 8 (complementary to (converted) top strand) GA/CT/GA: 10 (complementary to (converted) bottom strand) CT/GA/GA: 29787 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2557483 Total methylated C's in CpG context: 41376 Total methylated C's in CHG context: 3779 Total methylated C's in CHH context: 16013 Total methylated C's in Unknown context: 242 Total unmethylated C's in CpG context: 269479 Total unmethylated C's in CHG context: 418335 Total unmethylated C's in CHH context: 1808501 Total unmethylated C's in Unknown context: 7599 C methylated in CpG context: 13.3% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 3.1% Bismark completed in 0d 0h 0m 57s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/5902_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/5902_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/5902_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5902_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5902_R1.fq.gz Writing a C -> T converted version of the input file 5902_R1.fq.gz to 5902_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5902_R1.fq.gz to 5902_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5902_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5902_R2.fq.gz Writing a C -> T converted version of the input file 5902_R2.fq.gz to 5902_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5902_R2.fq.gz to 5902_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5902_R2.fq.gz (100001 sequences in total) Input files are 5902_R1.fq.gz_C_to_T.fastq and 5902_R1.fq.gz_G_to_A.fastq and 5902_R2.fq.gz_C_to_T.fastq and 5902_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 5902_R1.fq.gz_C_to_T.fastq and 5902_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:6:1101:5152:1309_1:N:0:NGTTCC/1 77 * 0 0 * * 0 0 GGTTTTTTGGGGTAGGGTAGGGTTATAGTAGGGGAATTAAGTTTTATATTGGAATATTTAGAGAAAATTTTTAAATTTTTTTTATAAAAATTATGATGTTTGGAAAGTTTAAATTAAAATGGATGTATTTTTAGGTAGTG JJAFJJJJJJJJJAFJJAFJAJ7AA7FA7->> Writing bisulfite mapping results to 5902_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5902_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5902_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99723 (99.72%) aligned concordantly 0 times 189 (0.19%) aligned concordantly exactly 1 time 88 (0.09%) aligned concordantly >1 times 0.28% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99735 (99.73%) aligned concordantly 0 times 172 (0.17%) aligned concordantly exactly 1 time 93 (0.09%) aligned concordantly >1 times 0.27% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 52886 (52.89%) aligned concordantly 0 times 22534 (22.53%) aligned concordantly exactly 1 time 24580 (24.58%) aligned concordantly >1 times 47.11% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 52898 (52.90%) aligned concordantly 0 times 22514 (22.51%) aligned concordantly exactly 1 time 24588 (24.59%) aligned concordantly >1 times 47.10% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5902_R1.fq.gz_C_to_T.fastq, 5902_R1.fq.gz_G_to_A.fastq, 5902_R2.fq.gz_C_to_T.fastq and 5902_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60658 Mapping efficiency: 60.7% Sequence pairs with no alignments under any condition: 29074 Sequence pairs did not map uniquely: 10268 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 30312 ((converted) top strand) GA/CT/CT: 6 (complementary to (converted) top strand) GA/CT/GA: 6 (complementary to (converted) bottom strand) CT/GA/GA: 30334 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2633532 Total methylated C's in CpG context: 38086 Total methylated C's in CHG context: 3652 Total methylated C's in CHH context: 16168 Total methylated C's in Unknown context: 288 Total unmethylated C's in CpG context: 276138 Total unmethylated C's in CHG context: 427634 Total unmethylated C's in CHH context: 1871854 Total unmethylated C's in Unknown context: 7589 C methylated in CpG context: 12.1% C methylated in CHG context: 0.8% C methylated in CHH context: 0.9% C methylated in unknown context (CN or CHN): 3.7% Bismark completed in 0d 0h 0m 54s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/5903_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/5903_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/5903_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5903_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5903_R1.fq.gz Writing a C -> T converted version of the input file 5903_R1.fq.gz to 5903_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5903_R1.fq.gz to 5903_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5903_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/5903_R2.fq.gz Writing a C -> T converted version of the input file 5903_R2.fq.gz to 5903_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file 5903_R2.fq.gz to 5903_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file 5903_R2.fq.gz (100001 sequences in total) Input files are 5903_R1.fq.gz_C_to_T.fastq and 5903_R1.fq.gz_G_to_A.fastq and 5903_R2.fq.gz_C_to_T.fastq and 5903_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from 5903_R1.fq.gz_C_to_T.fastq and 5903_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: GWNJ-0901:413:GW1904042006th:8:1101:11069:1327_1:N:0:NTGAAA/1 99 NC_047562.1_CT_converted 26539008 40 140M = 26539062 194 ATTTTTTAATTTATTATTAAATAAAAATTTTTAGTAAAATAAAATATTTAATAGGTTTGATGTTGATTGTTTATAGAAAGATGTTGGGTTGTTAGAGTTTATATAAGGTTTAGTTTTGTTTTTATATTTTGTTATAAATA JJJFJJJJJJJJFJAJ-AJF>> Writing bisulfite mapping results to 5903_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/5903_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/5903_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 99734 (99.73%) aligned concordantly 0 times 184 (0.18%) aligned concordantly exactly 1 time 82 (0.08%) aligned concordantly >1 times 0.27% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 99737 (99.74%) aligned concordantly 0 times 172 (0.17%) aligned concordantly exactly 1 time 91 (0.09%) aligned concordantly >1 times 0.26% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 53391 (53.39100000% reads; of these:) aligned concordantly 0 times 10000022194 ( (22.19%) aligned concordantly exactly 1 time 100.0024415% () were paired; of these:24.41 % ) aligned concordantly >1 times53584 (46.6153.58%% overall alignment rate) aligned concordantly 0 times 21967 (21.97%) aligned concordantly exactly 1 time 24449 (24.45%) aligned concordantly >1 times 46.42% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files 5903_R1.fq.gz_C_to_T.fastq, 5903_R1.fq.gz_G_to_A.fastq, 5903_R2.fq.gz_C_to_T.fastq and 5903_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 59448 Mapping efficiency: 59.4% Sequence pairs with no alignments under any condition: 30289 Sequence pairs did not map uniquely: 10263 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 29633 ((converted) top strand) GA/CT/CT: 4 (complementary to (converted) top strand) GA/CT/GA: 9 (complementary to (converted) bottom strand) CT/GA/GA: 29802 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2600619 Total methylated C's in CpG context: 38599 Total methylated C's in CHG context: 5298 Total methylated C's in CHH context: 22801 Total methylated C's in Unknown context: 306 Total unmethylated C's in CpG context: 279475 Total unmethylated C's in CHG context: 425432 Total unmethylated C's in CHH context: 1829014 Total unmethylated C's in Unknown context: 7537 C methylated in CpG context: 12.1% C methylated in CHG context: 1.2% C methylated in CHH context: 1.2% C methylated in unknown context (CN or CHN): 3.9% Bismark completed in 0d 0h 0m 55s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_10_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_10_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_10_R1.fq.gz Writing a C -> T converted version of the input file zr3534_10_R1.fq.gz to zr3534_10_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_10_R1.fq.gz to zr3534_10_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_10_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fq.gz Writing a C -> T converted version of the input file zr3534_10_R2.fq.gz to zr3534_10_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_10_R2.fq.gz to zr3534_10_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_10_R2.fq.gz (100001 sequences in total) Input files are zr3534_10_R1.fq.gz_C_to_T.fastq and zr3534_10_R1.fq.gz_G_to_A.fastq and zr3534_10_R2.fq.gz_C_to_T.fastq and zr3534_10_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_10_R1.fq.gz_C_to_T.fastq and zr3534_10_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1108:1000_1:N:0:ACAACTAC+NGTGATAA/1 77 * 0 0 * * 0 0 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGATTTTATAATAATATATATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFF,F,F:FFFFFFFFFFFFF:FF,:,,,F:,,FF,FF:F:FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1108:1000_2:N:0:ACAACTAC+NGTGATAA/2 141 * 0 0 * * 0 0 ATTTATATATCCATAATTATAACATCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATCTCT FFFFFF:FFFFF:FFFFFFFFFFFF:FFFFFF,:F:F:FFFFF:F,:::FF:F,F:F:::FFFFF:FFFFF:FFF:FFFFF,F,F,F:FFF:F::,:,F,F,,,,,F,F,,,, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_10_R1.fq.gz_G_to_A.fastq and zr3534_10_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1108:1000_1:N:0:ACAACTAC+NGTGATAA/1 99 NC_047564.1_GA_converted 7169120 0 1M5I100M1I8M = 7169121 109 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATTTTATAATAATATATATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFF,F,F:FFFFFFFFFFFFF:FF,:,,,F:,,FF,FF:F:FF AS:i:-52 XN:i:0 XM:i:4 XO:i:2 XG:i:6 NM:i:10 MD:Z:91A11T1C1T1 YS:i:-62 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1108:1000_2:N:0:ACAACTAC+NGTGATAA/2 147 NC_047564.1_GA_converted 7169121 0 96M11I6M = 7169120 -109 AAAAACATACACAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAATATTATAATTATAAATATATAAAT ,,,,F,F,,,,,F,F,:,::F:FFF:F,F,F,FFFFF:FFF:FFFFF:FFFFF:::F:F,F:FF:::,F:FFFFF:F:F:,FFFFFF:FFFFFFFFFFFF:FFFFF:FFFFFF AS:i:-62 XN:i:0 XM:i:4 XO:i:1 XG:i:11 NM:i:15 MD:Z:5A1A1A1A90 YS:i:-52 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_10_R1.fq.gz_G_to_A.fastq and zr3534_10_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1108:1000_1:N:0:ACAACTAC+NGTGATAA/1 83 NC_047567.1_CT_converted 9852871 0 4M1I5M2I103M = 9852871 -112 ATATATATATTATTATAAAATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT FF:F:FF,FF,,:F,,,:,FF:FFFFFFFFFFFFF:F,F,FFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-55 XN:i:0 XM:i:6 XO:i:2 XG:i:3 NM:i:9 MD:Z:2T3A95G2A0A3A1 YS:i:-63 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1108:1000_2:N:0:ACAACTAC+NGTGATAA/2 163 NC_047567.1_CT_converted 9852871 0 4M1I11M4I81M7I5M = 9852871 -112 ATTTATATATTTATAATTATAATATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTGTGTATGTTTTT FFFFFF:FFFFF:FFFFFFFFFFFF:FFFFFF,:F:F:FFFFF:F,:::FF:F,F:F:::FFFFF:FFFFF:FFF:FFFFF,F,F,F:FFF:F::,:,F,F,,,,,F,F,,,, AS:i:-63 XN:i:0 XM:i:2 XO:i:3 XG:i:12 NM:i:14 MD:Z:6A11T82 YS:i:-55 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_10_R1.fq.gz_C_to_T.fastq and zr3534_10_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1108:1000_1:N:0:ACAACTAC+NGTGATAA/1 77 * 0 0 * * 0 0 AGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAGAAAGAGAGAGAGAGAGAGAGATTTTATAATAATATATATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFF,F,F:FFFFFFFFFFFFF:FF,:,,,F:,,FF,FF:F:FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1108:1000_2:N:0:ACAACTAC+NGTGATAA/2 141 * 0 0 * * 0 0 ATTTATATATCCATAATTATAACATCTCTCTCTCTCTCTCTCTTTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTATATATATCTCT FFFFFF:FFFFF:FFFFFFFFFFFF:FFFFFF,:F:F:FFFFF:F,:::FF:F,F:F:::FFFFF:FFFFF:FFF:FFFFF,F,F,F:FFF:F::,:,F,F,,,,,F,F,,,, YT:Z:UP >>> Writing bisulfite mapping results to zr3534_10_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_10_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72823 (72.82%) aligned concordantly 0 times 12231 (12.23%) aligned concordantly exactly 1 time 14946 (14.95%) aligned concordantly >1 times 27.18% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72944 (72.94%) aligned concordantly 0 times 12187 (12.19%) aligned concordantly exactly 1 time 14869 (14.87%) aligned concordantly >1 times 27.06% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72995 (73.00%) aligned concordantly 0 times 12101 (12.10%) aligned concordantly exactly 1 time 14904 (14.90%) aligned concordantly >1 times 27.00% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73189 (73.19%) aligned concordantly 0 times 12009 (12.01%) aligned concordantly exactly 1 time 14802 (14.80%) aligned concordantly >1 times 26.81% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_10_R1.fq.gz_C_to_T.fastq, zr3534_10_R1.fq.gz_G_to_A.fastq, zr3534_10_R2.fq.gz_C_to_T.fastq and zr3534_10_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61864 Mapping efficiency: 61.9% Sequence pairs with no alignments under any condition: 21587 Sequence pairs did not map uniquely: 16549 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15259 ((converted) top strand) GA/CT/CT: 15471 (complementary to (converted) top strand) GA/CT/GA: 15577 (complementary to (converted) bottom strand) CT/GA/GA: 15557 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2178047 Total methylated C's in CpG context: 28747 Total methylated C's in CHG context: 1738 Total methylated C's in CHH context: 7062 Total methylated C's in Unknown context: 79 Total unmethylated C's in CpG context: 256943 Total unmethylated C's in CHG context: 382808 Total unmethylated C's in CHH context: 1500749 Total unmethylated C's in Unknown context: 5375 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fq.gz Writing a C -> T converted version of the input file zr3534_1_R1.fq.gz to zr3534_1_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_1_R1.fq.gz to zr3534_1_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_1_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fq.gz Writing a C -> T converted version of the input file zr3534_1_R2.fq.gz to zr3534_1_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_1_R2.fq.gz to zr3534_1_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_1_R2.fq.gz (100001 sequences in total) Input files are zr3534_1_R1.fq.gz_C_to_T.fastq and zr3534_1_R1.fq.gz_G_to_A.fastq and zr3534_1_R2.fq.gz_C_to_T.fastq and zr3534_1_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_1_R1.fq.gz_C_to_T.fastq and zr3534_1_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1253:1000_1:N:0:CTCGAATA+NCGACATC/1 77 * 0 0 * * 0 0 ATTGATTTGTGTTTTGTGGTAGTTGTAGTTTTTAATTTGGTGTTTTATTAGATTTGTTTTTATTATAGTGTTGTTTTTTAATTATTTTTAAAT FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1253:1000_2:N:0:CTCGAATA+NCGACATC/2 141 * 0 0 * * 0 0 AATTAAAAAACAACACTATAATAAAAACAAATCTAATAAAACACCAAATTAAAAACTACAACTACCACAAAACACAAATCAATCAAAAAACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_1_R1.fq.gz_G_to_A.fastq and zr3534_1_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1253:1000_1:N:0:CTCGAATA+NCGACATC/1 77 * 0 0 * * 0 0 ATTAATTTATATTTTATAATAATTATAATTTTTAATCTAATATTTTATTAAATTTATTTTTATTATAATATTATTTTTTAATTATTTTTAAAT FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1253:1000_2:N:0:CTCGAATA+NCGACATC/2 141 * 0 0 * * 0 0 AATTAAAAAATAATATTATAATAAAAATAAATTTAATAAAATATTAGATTAAAAATTATAATTATTATAAAATATAAATTAATTAAAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_1_R1.fq.gz_G_to_A.fastq and zr3534_1_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1253:1000_1:N:0:CTCGAATA+NCGACATC/1 77 * 0 0 * * 0 0 ATTAATTTATATTTTATAATAATTATAATTTTTAATCTAATATTTTATTAAATTTATTTTTATTATAATATTATTTTTTAATTATTTTTAAAT FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1253:1000_2:N:0:CTCGAATA+NCGACATC/2 141 * 0 0 * * 0 0 AATTAAAAAATAATATTATAATAAAAATAAATTTAATAAAATATTAGATTAAAAATTATAATTATTATAAAATATAAATTAATTAAAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_1_R1.fq.gz_C_to_T.fastq and zr3534_1_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1253:1000_1:N:0:CTCGAATA+NCGACATC/1 83 NC_047565.1_GA_converted 3976990 23 38M1I54M = 3977000 102 ATTTAAAAATAATTAAAAAACAACACTATAATAAAAACAAATCTAATAAAACACCAAATTAAAAACTACAACTACCACAAAACACAAATCAAT F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF AS:i:-38 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:1A0A0A0C50T36 YS:i:-14 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1253:1000_2:N:0:CTCGAATA+NCGACATC/2 163 NC_047565.1_GA_converted 3977000 23 28M1I64M = 3976990 -102 AATTAAAAAACAACACTATAATAAAAACAAATCTAATAAAACACCAAATTAAAAACTACAACTACCACAAAACACAAATCAATCAAAAAACAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFF:FF:FFF AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:45T46 YS:i:-38 YT:Z:CP >>> Writing bisulfite mapping results to zr3534_1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73276 (73.28%) aligned concordantly 0 times 12286 (12.29%) aligned concordantly exactly 1 time 14438 (14.44%) aligned concordantly >1 times 26.72% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73355 (73.36%) aligned concordantly 0 times 12151 (12.15%) aligned concordantly exactly 1 time 14494 (14.49%) aligned concordantly >1 times 26.64% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73397 (73.40%) aligned concordantly 0 times 12058 (12.06%) aligned concordantly exactly 1 time 14545 (10000014.54 reads; of these:% ) aligned concordantly >1 times 10000026.60 (% overall alignment rate 100.00%) were paired; of these: 73546 (73.55%) aligned concordantly 0 times 12058 (12.06%) aligned concordantly exactly 1 time 14396 (14.40%) aligned concordantly >1 times 26.45% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_1_R1.fq.gz_C_to_T.fastq, zr3534_1_R1.fq.gz_G_to_A.fastq, zr3534_1_R2.fq.gz_C_to_T.fastq and zr3534_1_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61618 Mapping efficiency: 61.6% Sequence pairs with no alignments under any condition: 22474 Sequence pairs did not map uniquely: 15908 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15265 ((converted) top strand) GA/CT/CT: 15548 (complementary to (converted) top strand) GA/CT/GA: 15353 (complementary to (converted) bottom strand) CT/GA/GA: 15452 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2147800 Total methylated C's in CpG context: 28863 Total methylated C's in CHG context: 1776 Total methylated C's in CHH context: 7687 Total methylated C's in Unknown context: 61 Total unmethylated C's in CpG context: 251766 Total unmethylated C's in CHG context: 374609 Total unmethylated C's in CHH context: 1483099 Total unmethylated C's in Unknown context: 5309 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fq.gz Writing a C -> T converted version of the input file zr3534_2_R1.fq.gz to zr3534_2_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_2_R1.fq.gz to zr3534_2_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_2_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fq.gz Writing a C -> T converted version of the input file zr3534_2_R2.fq.gz to zr3534_2_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_2_R2.fq.gz to zr3534_2_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_2_R2.fq.gz (100001 sequences in total) Input files are zr3534_2_R1.fq.gz_C_to_T.fastq and zr3534_2_R1.fq.gz_G_to_A.fastq and zr3534_2_R2.fq.gz_C_to_T.fastq and zr3534_2_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_2_R1.fq.gz_C_to_T.fastq and zr3534_2_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:4444:1423_1:N:0:GATCGTCG+ACATATCC/1 77 * 0 0 * * 0 0 ATAAAATATTAATAAATTAATTAAATAATTTTAAAATTAATAAATAATAAAAATTTAAAATAATATAATATATTTTATTTTAATTAAAATATAATAATAATTTTTAAAATATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:4444:1423_2:N:0:GATCGTCG+ACATATCC/2 141 * 0 0 * * 0 0 TTATTTTTATTATTTAAATATATTAAAAAATTTAAAAAATTTTTATTATTAATAATTAATTTATTATTTTATTATAAAATTTTATTTTAATAAAATATATTAATAAAATTTAAT FFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFF:FF:FFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_2_R1.fq.gz_G_to_A.fastq and zr3534_2_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:4444:1423_1:N:0:GATCGTCG+ACATATCC/1 99 NC_047562.1_GA_converted 34078973 42 115M = 34079087 228 ACAAAATATTAACAAATTAACCAAACAACTTTAAAATCAACAAACAACAAAAATTTAAAATAATACAACATATTTTACTTCAATCAAAATATAATAACAATCCTCAAAATACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:115 YS:i:0 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:4444:1423_2:N:0:GATCGTCG+ACATATCC/2 147 NC_047562.1_GA_converted 34079087 42 114M = 34078973 -228 ACTAAATTTCATCAATATATTCCATCAAAATAAAATTTTATAACAAAACAACAAATTAATTACCAACAATAAAAATTCTCTAAATTCCTTAATATATTTAAATAATAAAAACAA FFFFFFFF:FF:FFFFFFFFFF,FFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFF,FFFFFFFFFFFFF:FFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:114 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_2_R1.fq.gz_G_to_A.fastq and zr3534_2_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:4444:1423_1:N:0:GATCGTCG+ACATATCC/1 77 * 0 0 * * 0 0 ACAAAATATTAACAAATTAACCAAACAACTTTAAAATCAACAAACAACAAAAATTTAAAATAATACAACATATTTTACTTCAATCAAAATATAATAACAATCCTCAAAATACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:4444:1423_2:N:0:GATCGTCG+ACATATCC/2 141 * 0 0 * * 0 0 TTGTTTTTATTATTTAAATATATTAAGGAATTTAGAGAATTTTTATTGTTGGTAATTAATTTGTTGTTTTGTTATAAAATTTTATTTTGATGGAATATATTGATGAAATTTAGT FFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFF:FF:FFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_2_R1.fq.gz_C_to_T.fastq and zr3534_2_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:4444:1423_1:N:0:GATCGTCG+ACATATCC/1 77 * 0 0 * * 0 0 ATAAAATATTAATAAATTAATTAAATAATTTTAAAATTAATAAATAATAAAAATTTAAAATAATATAATATATTTTATTTTAATTAAAATATAATAATAATTTTTAAAATATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF::FFFF:FFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:4444:1423_2:N:0:GATCGTCG+ACATATCC/2 141 * 0 0 * * 0 0 TTATTTTTATTATTTAAATATATTAAAAAATTTAAAAAATTTTTATTATTAATAATTAATTTATTATTTTATTATAAAATTTTATTTTAATAAAATATATTAATAAAATTTAAT FFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFF:FFFFFFFFFFFFF,FFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFF,FFFFFFFFFF:FF:FFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3534_2_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73168 (73.17%) aligned concordantly 0 times 12118 (12.12%) aligned concordantly exactly 1 time 14714 (14.71%) aligned concordantly >1 times 26.83% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72973 (72.97%) aligned concordantly 0 times 12284 (12.28%) aligned concordantly exactly 1 time 14743 (14.74%) aligned concordantly >1 times 27.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73252 (73.25%) aligned concordantly 0 times 12070 (12.07%) aligned concordantly exactly 1 time 14678 (14.68%) aligned concordantly >1 times 26.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73478 (73.48%) aligned concordantly 0 times 11826 (11.83%) aligned concordantly exactly 1 time 14696 (14.70%) aligned concordantly >1 times 26.52% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_2_R1.fq.gz_C_to_T.fastq, zr3534_2_R1.fq.gz_G_to_A.fastq, zr3534_2_R2.fq.gz_C_to_T.fastq and zr3534_2_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61056 Mapping efficiency: 61.1% Sequence pairs with no alignments under any condition: 22398 Sequence pairs did not map uniquely: 16546 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15479 ((converted) top strand) GA/CT/CT: 15217 (complementary to (converted) top strand) GA/CT/GA: 15036 (complementary to (converted) bottom strand) CT/GA/GA: 15324 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2137198 Total methylated C's in CpG context: 28100 Total methylated C's in CHG context: 1748 Total methylated C's in CHH context: 7871 Total methylated C's in Unknown context: 52 Total unmethylated C's in CpG context: 252518 Total unmethylated C's in CHG context: 373045 Total unmethylated C's in CHH context: 1473916 Total unmethylated C's in Unknown context: 5087 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.0% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_3_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_3_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_3_R1.fq.gz Writing a C -> T converted version of the input file zr3534_3_R1.fq.gz to zr3534_3_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_3_R1.fq.gz to zr3534_3_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_3_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fq.gz Writing a C -> T converted version of the input file zr3534_3_R2.fq.gz to zr3534_3_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_3_R2.fq.gz to zr3534_3_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_3_R2.fq.gz (100001 sequences in total) Input files are zr3534_3_R1.fq.gz_C_to_T.fastq and zr3534_3_R1.fq.gz_G_to_A.fastq and zr3534_3_R2.fq.gz_C_to_T.fastq and zr3534_3_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_3_R1.fq.gz_C_to_T.fastq and zr3534_3_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1561:1000_1:N:0:TATCCGAG+NTTATTGG/1 77 * 0 0 * * 0 0 TATATAATTAATTTTTATTTTTTAATATATATTATAATTTTTATTAATATTATAATTAAAAAAAATTATTATTAATAAAAATTAAAAAATTATAAATATTAATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1561:1000_2:N:0:TATCCGAG+NTTATTGG/2 141 * 0 0 * * 0 0 ATTTATAATTTTTTAATTTTTATTAATAATAATTTTTTTTAATTATAATATTAATAAAAATTATAATATATATTAAAAAATAAAAATTAATTATATAATTATTATAA FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFF,FFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_3_R1.fq.gz_G_to_A.fastq and zr3534_3_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1561:1000_1:N:0:TATCCGAG+NTTATTGG/1 77 * 0 0 * * 0 0 CATACAATTAACTTTTATCTTTTAATATATACCATAACTTCTATTAACACTATAATCAAAAAAAACTACTACCAACAAAAATTAAAAAACTACAAACACTAATACCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1561:1000_2:N:0:TATCCGAG+NTTATTGG/2 141 * 0 0 * * 0 0 GTTTGTAGTTTTTTAATTTTTGTTGGTAGTAGTTTTTTTTGATTATAGTGTTAATAGAAGTTATGGTATATATTAAAAGATAAAAGTTAATTGTATGATTGTTGTGA FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFF,FFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_3_R1.fq.gz_G_to_A.fastq and zr3534_3_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1561:1000_1:N:0:TATCCGAG+NTTATTGG/1 77 * 0 0 * * 0 0 CATACAATTAACTTTTATCTTTTAATATATACCATAACTTCTATTAACACTATAATCAAAAAAAACTACTACCAACAAAAATTAAAAAACTACAAACACTAATACCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1561:1000_2:N:0:TATCCGAG+NTTATTGG/2 141 * 0 0 * * 0 0 GTTTGTAGTTTTTTAATTTTTGTTGGTAGTAGTTTTTTTTGATTATAGTGTTAATAGAAGTTATGGTATATATTAAAAGATAAAAGTTAATTGTATGATTGTTGTGA FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFF,FFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_3_R1.fq.gz_C_to_T.fastq and zr3534_3_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1561:1000_1:N:0:TATCCGAG+NTTATTGG/1 77 * 0 0 * * 0 0 TATATAATTAATTTTTATTTTTTAATATATATTATAATTTTTATTAATATTATAATTAAAAAAAATTATTATTAATAAAAATTAAAAAATTATAAATATTAATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1561:1000_2:N:0:TATCCGAG+NTTATTGG/2 141 * 0 0 * * 0 0 ATTTATAATTTTTTAATTTTTATTAATAATAATTTTTTTTAATTATAATATTAATAAAAATTATAATATATATTAAAAAATAAAAATTAATTATATAATTATTATAA FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF,FFF,FFFF:F YT:Z:UP >>> Writing bisulfite mapping results to zr3534_3_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_3_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73647 (73.65%) aligned concordantly 0 times 11825 (11.82%) aligned concordantly exactly 1 time 14528 (14.53%) aligned concordantly >1 times 26.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73621 (73.62%) aligned concordantly 0 times 12033 (12.03%) aligned concordantly exactly 1 time 14346 (14.35%) aligned concordantly >1 times 26.38% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73548 (73.55%) aligned concordantly 0 times 12037 (12.04%) aligned concordantly exactly 1 time 14415 (14.41%) aligned concordantly >1 times 26.45% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73494 (73.49%) aligned concordantly 0 times 12000 (12.00%) aligned concordantly exactly 1 time 14506 (14.51%) aligned concordantly >1 times 26.51% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_3_R1.fq.gz_C_to_T.fastq, zr3534_3_R1.fq.gz_G_to_A.fastq, zr3534_3_R2.fq.gz_C_to_T.fastq and zr3534_3_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60805 Mapping efficiency: 60.8% Sequence pairs with no alignments under any condition: 23295 Sequence pairs did not map uniquely: 15900 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15213 ((converted) top strand) GA/CT/CT: 15176 (complementary to (converted) top strand) GA/CT/GA: 15206 (complementary to (converted) bottom strand) CT/GA/GA: 15210 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2125117 Total methylated C's in CpG context: 32587 Total methylated C's in CHG context: 1966 Total methylated C's in CHH context: 8237 Total methylated C's in Unknown context: 79 Total unmethylated C's in CpG context: 241674 Total unmethylated C's in CHG context: 368620 Total unmethylated C's in CHH context: 1472033 Total unmethylated C's in Unknown context: 5484 C methylated in CpG context: 11.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_4_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_4_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_4_R1.fq.gz Writing a C -> T converted version of the input file zr3534_4_R1.fq.gz to zr3534_4_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_4_R1.fq.gz to zr3534_4_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_4_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fq.gz Writing a C -> T converted version of the input file zr3534_4_R2.fq.gz to zr3534_4_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_4_R2.fq.gz to zr3534_4_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_4_R2.fq.gz (100001 sequences in total) Input files are zr3534_4_R1.fq.gz_C_to_T.fastq and zr3534_4_R1.fq.gz_G_to_A.fastq and zr3534_4_R2.fq.gz_C_to_T.fastq and zr3534_4_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_4_R1.fq.gz_C_to_T.fastq and zr3534_4_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1796:1000_1:N:0:CGCTGTCT+NGTGAGTA/1 77 * 0 0 * * 0 0 ATAGAATGAAGTTTAATTAAATGTATATATGAGAATTATTAAAAGGTTTGTATGGGTTATAGAAATTGTTAAGGATTGTTTATTTTTTGTAAGATTTTTTTATTTTTTAGGTGAA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF,FF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1796:1000_2:N:0:CGCTGTCT+NGTGAGTA/2 141 * 0 0 * * 0 0 AATCATCTTTAAATTCTCCCTAAAAATAACTTAAAAATACAAAACAAAAAAATCAAAAAATCTTTCACCTAAAAAATAAAAAAATCTTACAAAAAATAAACAATCCTTAACAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFFFFFFFFFF:F:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_4_R1.fq.gz_G_to_A.fastq and zr3534_4_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1796:1000_1:N:0:CGCTGTCT+NGTGAGTA/1 77 * 0 0 * * 0 0 ATAAAATAAAATTTAATTAAATATATATATAAAAATTATTAAAAAATTTATATAAATTATAAAAATTATTAAAAATTATTTATTTTTTATAAAATTTTTTTATTTTTTAAATAAA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF,FF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1796:1000_2:N:0:CGCTGTCT+NGTGAGTA/2 141 * 0 0 * * 0 0 AATTATTTTTAAATTTTTTTTAAAAATAATTTAAAAATATAAAATAAAAAAATTAAAAAATTTTTTATTTAAAAAATAAAAAAATTTTATAAAAAATAAATAATTTTTAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFFFFFFFFFF:F:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_4_R1.fq.gz_G_to_A.fastq and zr3534_4_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1796:1000_1:N:0:CGCTGTCT+NGTGAGTA/1 77 * 0 0 * * 0 0 ATAAAATAAAATTTAATTAAATATATATATAAAAATTATTAAAAAATTTATATAAATTATAAAAATTATTAAAAATTATTTATTTTTTATAAAATTTTTTTATTTTTTAAATAAA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF,FF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1796:1000_2:N:0:CGCTGTCT+NGTGAGTA/2 141 * 0 0 * * 0 0 AATTATTTTTAAATTTTTTTTAAAAATAATTTAAAAATATAAAATAAAAAAATTAAAAAATTTTTTATTTAAAAAATAAAAAAATTTTATAAAAAATAAATAATTTTTAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFFFFFFFFFF:F:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_4_R1.fq.gz_C_to_T.fastq and zr3534_4_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1796:1000_1:N:0:CGCTGTCT+NGTGAGTA/1 77 * 0 0 * * 0 0 ATAGAATGAAGTTTAATTAAATGTATATATGAGAATTATTAAAAGGTTTGTATGGGTTATAGAAATTGTTAAGGATTGTTTATTTTTTGTAAGATTTTTTTATTTTTTAGGTGAA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFF,FF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1796:1000_2:N:0:CGCTGTCT+NGTGAGTA/2 141 * 0 0 * * 0 0 AATCATCTTTAAATTCTCCCTAAAAATAACTTAAAAATACAAAACAAAAAAATCAAAAAATCTTTCACCTAAAAAATAAAAAAATCTTACAAAAAATAAACAATCCTTAACAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF,FFFF:F:FFFFFFFFFFFFFFFF:F:F YT:Z:UP >>> Writing bisulfite mapping results to zr3534_4_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_4_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1101:27272:31219_1:N:0:CGCTGTCT+GGTGAGTA NW_022994966.1 1 100000 reads; of these: 100000 (100.00%) were paired; of these: 73186 (73.19%) aligned concordantly 0 times 12219 (12.22%) aligned concordantly exactly 1 time 14595 (14.60%) aligned concordantly >1 times 26.81% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73219 (73.22%) aligned concordantly 0 times 12183 (12.18%) aligned concordantly exactly 1 time 14598 (14.60%) aligned concordantly >1 times 26.78% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73060 (73.06%) aligned concordantly 0 times 12296 (12.30%) aligned concordantly exactly 1 time 14644 (14.64%) aligned concordantly >1 times 26.94% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73343 (73.34%) aligned concordantly 0 times 12095 (12.10%) aligned concordantly exactly 1 time 14562 (14.56%) aligned concordantly >1 times 26.66% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_4_R1.fq.gz_C_to_T.fastq, zr3534_4_R1.fq.gz_G_to_A.fastq, zr3534_4_R2.fq.gz_C_to_T.fastq and zr3534_4_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61752 Mapping efficiency: 61.8% Sequence pairs with no alignments under any condition: 22130 Sequence pairs did not map uniquely: 16118 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15331 ((converted) top strand) GA/CT/CT: 15379 (complementary to (converted) top strand) GA/CT/GA: 15518 (complementary to (converted) bottom strand) CT/GA/GA: 15523 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2153460 Total methylated C's in CpG context: 31225 Total methylated C's in CHG context: 1738 Total methylated C's in CHH context: 8146 Total methylated C's in Unknown context: 84 Total unmethylated C's in CpG context: 248966 Total unmethylated C's in CHG context: 375718 Total unmethylated C's in CHH context: 1487667 Total unmethylated C's in Unknown context: 5212 C methylated in CpG context: 11.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fq.gz Writing a C -> T converted version of the input file zr3534_5_R1.fq.gz to zr3534_5_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_5_R1.fq.gz to zr3534_5_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_5_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fq.gz Writing a C -> T converted version of the input file zr3534_5_R2.fq.gz to zr3534_5_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_5_R2.fq.gz to zr3534_5_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_5_R2.fq.gz (100001 sequences in total) Input files are zr3534_5_R1.fq.gz_C_to_T.fastq and zr3534_5_R1.fq.gz_G_to_A.fastq and zr3534_5_R2.fq.gz_C_to_T.fastq and zr3534_5_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_5_R1.fq.gz_C_to_T.fastq and zr3534_5_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1759:1000_1:N:0:AATGCGAA+NCCGCCAA/1 77 * 0 0 * * 0 0 AAATTTAATGAAAAATTATTTATATTATAATATATATATATATATTTATATTTTATATAATATTTAAATAATTAATTTTATTATAATTTAATATATTAAAATATATTTTTTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1759:1000_2:N:0:AATGCGAA+NCCGCCAA/2 141 * 0 0 * * 0 0 TATATTATATTAAAAAAATATAATATTTTTATAAAAAATTTATATATATTAAATAATATTAAAAAATATATTTTAATATATTAAATTATAATAAAATTAATTATTTAAATATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_5_R1.fq.gz_G_to_A.fastq and zr3534_5_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1759:1000_1:N:0:AATGCGAA+NCCGCCAA/1 77 * 0 0 * * 0 0 AAACTCAATAAAAAATCACTTATATCACAATATATATATATATATTCACACTTTATACAATACTTAAATAACTAACCCTACTATAATTTAACATATTAAAATACACTTTCCAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1759:1000_2:N:0:AATGCGAA+NCCGCCAA/2 141 * 0 0 * * 0 0 TATATTGTATTAAAAAAGTATGGTATTTTTATAAGGAATTTGTGTATGTTAAATAATGTTGGAAAGTGTATTTTAATATGTTAAATTATAGTAGGGTTAGTTATTTAAGTATTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_5_R1.fq.gz_G_to_A.fastq and zr3534_5_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1759:1000_1:N:0:AATGCGAA+NCCGCCAA/1 77 * 0 0 * * 0 0 AAACTCAATAAAAAATCACTTATATCACAATATATATATATATATTCACACTTTATACAATACTTAAATAACTAACCCTACTATAATTTAACATATTAAAATACACTTTCCAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1759:1000_2:N:0:AATGCGAA+NCCGCCAA/2 141 * 0 0 * * 0 0 TATATTGTATTAAAAAAGTATGGTATTTTTATAAGGAATTTGTGTATGTTAAATAATGTTGGAAAGTGTATTTTAATATGTTAAATTATAGTAGGGTTAGTTATTTAAGTATTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_5_R1.fq.gz_C_to_T.fastq and zr3534_5_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1759:1000_1:N:0:AATGCGAA+NCCGCCAA/1 77 * 0 0 * * 0 0 AAATTTAATGAAAAATTATTTATATTATAATATATATATATATATTTATATTTTATATAATATTTAAATAATTAATTTTATTATAATTTAATATATTAAAATATATTTTTTAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1759:1000_2:N:0:AATGCGAA+NCCGCCAA/2 141 * 0 0 * * 0 0 TATATTATATTAAAAAAATATAATATTTTTATAAAAAATTTATATATATTAAATAATATTAAAAAATATATTTTAATATATTAAATTATAATAAAATTAATTATTTAAATATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF,F YT:Z:UP >>> Writing bisulfite mapping results to zr3534_5_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73315 (73.31%) aligned concordantly 0 times 11837 (11.84%) aligned concordantly exactly 1 time 14848 (14.85%) aligned concordantly >1 times 26.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72882 (72.88%) aligned concordantly 0 times 12135 (12.13%) aligned concordantly exactly 1 time 14983 (14.98%) aligned concordantly >1 times 27.12% overall alignment rate 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (73297 (73.30%) aligned concordantly 0 times 11990 (11.99%) aligned concordantly exactly 1 time 100.00 %14713) were paired; of these: ( 14.71 %72961) aligned concordantly >1 times ( 72.9626.70%%) aligned concordantly 0 times overall alignment rate 12130 (12.13%) aligned concordantly exactly 1 time 14909 (14.91%) aligned concordantly >1 times 27.04% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_5_R1.fq.gz_C_to_T.fastq, zr3534_5_R1.fq.gz_G_to_A.fastq, zr3534_5_R2.fq.gz_C_to_T.fastq and zr3534_5_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61435 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 22294 Sequence pairs did not map uniquely: 16271 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15396 ((converted) top strand) GA/CT/CT: 15226 (complementary to (converted) top strand) GA/CT/GA: 15288 (complementary to (converted) bottom strand) CT/GA/GA: 15525 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2137438 Total methylated C's in CpG context: 31070 Total methylated C's in CHG context: 1884 Total methylated C's in CHH context: 8105 Total methylated C's in Unknown context: 60 Total unmethylated C's in CpG context: 244356 Total unmethylated C's in CHG context: 371466 Total unmethylated C's in CHH context: 1480557 Total unmethylated C's in Unknown context: 5408 C methylated in CpG context: 11.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_6_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_6_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_6_R1.fq.gz Writing a C -> T converted version of the input file zr3534_6_R1.fq.gz to zr3534_6_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_6_R1.fq.gz to zr3534_6_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_6_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fq.gz Writing a C -> T converted version of the input file zr3534_6_R2.fq.gz to zr3534_6_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_6_R2.fq.gz to zr3534_6_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_6_R2.fq.gz (100001 sequences in total) Input files are zr3534_6_R1.fq.gz_C_to_T.fastq and zr3534_6_R1.fq.gz_G_to_A.fastq and zr3534_6_R2.fq.gz_C_to_T.fastq and zr3534_6_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_6_R1.fq.gz_C_to_T.fastq and zr3534_6_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1651:1000_1:N:0:AATTCTTG+NAGTTGAC/1 99 NC_047563.1_CT_converted 51781561 0 94M = 51781551 -104 TTTTTTGGATTTTTTATTTGAGGGGTTAGTTTTTTTTTTTTGATTTTAAAGAAAATGTTTTGTAAAAAGAAATTTTTTGTATATTATATGTTTT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFF,FFFFFFFFFFFFFFFFFFFF,FFFF AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:8T57T11T15 YS:i:-24 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1651:1000_2:N:0:AATTCTTG+NAGTTGAC/2 147 NC_047563.1_CT_converted 51781551 0 94M = 51781561 104 GATTTTAAAGTTTTTTGGATTTTTTATTTGAGGGGTTAGTTTTTTTTTTTTGATTTTAAAGAAAATGTTTTGTAAAAAGAAATTTTTTGTATAT ,F:FF::FF:::::,,F:F:FF:F:F,FFFF:F,F:FFF,FFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:7G10T57T11T5 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_6_R1.fq.gz_G_to_A.fastq and zr3534_6_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1651:1000_1:N:0:AATTCTTG+NAGTTGAC/1 77 * 0 0 * * 0 0 TTTTTTAAATTTTTTATTTAAAAAATTAATTTTTTTTTTTTAATTTTAAAAAAAATATTTTATAAAAAAAAATTTTTTATATATTATATATTTT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFF,FFFFFFFFFFFFFFFFFFFF,FFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1651:1000_2:N:0:AATTCTTG+NAGTTGAC/2 141 * 0 0 * * 0 0 ATATATAAAAAATTTTTTTTTATAAAATATTTTTTTTAAAATTAAAAAAAAAAAATTAATTTTTTAAATAAAAAATTTAAAAAATTTTAAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFF,FFF:F,F:FFFF,F:F:FF:F:F,,:::::FF::FF:F, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_6_R1.fq.gz_G_to_A.fastq and zr3534_6_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1651:1000_1:N:0:AATTCTTG+NAGTTGAC/1 77 * 0 0 * * 0 0 TTTTTTAAATTTTTTATTTAAAAAATTAATTTTTTTTTTTTAATTTTAAAAAAAATATTTTATAAAAAAAAATTTTTTATATATTATATATTTT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFF,FFFFFFFFFFF,FFFFFF,FFFFFFFFFFFFFFFFFFFF,FFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1651:1000_2:N:0:AATTCTTG+NAGTTGAC/2 141 * 0 0 * * 0 0 ATATATAAAAAATTTTTTTTTATAAAATATTTTTTTTAAAATTAAAAAAAAAAAATTAATTTTTTAAATAAAAAATTTAAAAAATTTTAAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFF,FFF:F,F:FFFF,F:F:FF:F:F,,:::::FF::FF:F, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_6_R1.fq.gz_C_to_T.fastq and zr3534_6_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1651:1000_1:N:0:AATTCTTG+NAGTTGAC/1 83 NC_047563.1_GA_converted 8169680 0 94M = 8169690 104 AAAACATATAATATACAAAAAATTTCTTTTTACAAAACATTTTCTTTAAAATCAAAAAAAAAAAACTAACCCCTCAAATAAAAAATCCAAAAAA FFFF,FFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFF,FFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:15A11A57A8 YS:i:-24 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1651:1000_2:N:0:AATTCTTG+NAGTTGAC/2 163 NC_047563.1_GA_converted 8169690 0 94M = 8169680 -104 ATATACAAAAAATTTCTTTTTACAAAACATTTTCTTTAAAATCAAAAAAAAAAAACTAACCCCTCAAATAAAAAATCCAAAAAACTTTAAAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFFFFF,FFF:F,F:FFFF,F:F:FF:F:F,,:::::FF::FF:F, AS:i:-24 XS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:5A11A57A10C7 YS:i:-18 YT:Z:CP >>> Writing bisulfite mapping results to zr3534_6_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_6_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73654 (73.65%) aligned concordantly 0 times 12030 (12.03%) aligned concordantly exactly 1 time 14316 (14.32%) aligned concordantly >1 times 26.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73571 (73.57%) aligned concordantly 0 times 11995 (11.99%) aligned concordantly exactly 1 time 14434 (14.43%) aligned concordantly >1 times 26.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73664 (73.66%) aligned concordantly 0 times 11992 (11.99%) aligned concordantly exactly 1 time 14344 (14.34%) aligned concordantly >1 times 26.34% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73706 (73.71%) aligned concordantly 0 times 12012 (12.01%) aligned concordantly exactly 1 time 14282 (14.28%) aligned concordantly >1 times 26.29% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_6_R1.fq.gz_C_to_T.fastq, zr3534_6_R1.fq.gz_G_to_A.fastq, zr3534_6_R2.fq.gz_C_to_T.fastq and zr3534_6_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60946 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 23409 Sequence pairs did not map uniquely: 15645 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15361 ((converted) top strand) GA/CT/CT: 15232 (complementary to (converted) top strand) GA/CT/GA: 15290 (complementary to (converted) bottom strand) CT/GA/GA: 15063 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2131023 Total methylated C's in CpG context: 28664 Total methylated C's in CHG context: 1772 Total methylated C's in CHH context: 7458 Total methylated C's in Unknown context: 59 Total unmethylated C's in CpG context: 247062 Total unmethylated C's in CHG context: 369466 Total unmethylated C's in CHH context: 1476601 Total unmethylated C's in Unknown context: 5369 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_7_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_7_R1.fq.gz Writing a C -> T converted version of the input file zr3534_7_R1.fq.gz to zr3534_7_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_7_R1.fq.gz to zr3534_7_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_7_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fq.gz Writing a C -> T converted version of the input file zr3534_7_R2.fq.gz to zr3534_7_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_7_R2.fq.gz to zr3534_7_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_7_R2.fq.gz (100001 sequences in total) Input files are zr3534_7_R1.fq.gz_C_to_T.fastq and zr3534_7_R1.fq.gz_G_to_A.fastq and zr3534_7_R2.fq.gz_C_to_T.fastq and zr3534_7_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_7_R1.fq.gz_C_to_T.fastq and zr3534_7_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1723:1000_1:N:0:TTCCTACA+NGAATTCG/1 77 * 0 0 * * 0 0 TTTTTAATTAAAATAATTTTTTTTAAAATTATATATTATTTTATTTAATTTATTAATAAATAATATTATTTTTTAAAAAAAAAAATTTTTTTTAAAATTATATAATAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1723:1000_2:N:0:TTCCTACA+NGAATTCG/2 141 * 0 0 * * 0 0 TTTTAATTTTTATTATATAATTTTAAAAAAAATTTTTTTTTTTAAAAAATTATATTATTTATTAATAAATTAAATAAAATAATATTTAATTTTAAAAAAAATTATTTTAATTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFFF,FFF:FFFFFFF,FFFFFFFFF,FFFFFFFF:FFFFFFFF,FFFFFFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_7_R1.fq.gz_G_to_A.fastq and zr3534_7_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1723:1000_1:N:0:TTCCTACA+NGAATTCG/1 77 * 0 0 * * 0 0 TTTTCAATTAAAACAATTTTTCCTAAAATTACATATTATCTCATTTAATCCATCAATAAATAATATCATTTTTCAAAAAAAAAAATTTTTCCCAAAATCACATAATAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1723:1000_2:N:0:TTCCTACA+NGAATTCG/2 141 * 0 0 * * 0 0 TTTTAATTTTTATTATGTGATTTTGGGAAAAATTTTTTTTTTTGAAAAATTATATTATTTATTGATGGATTAAATGAGATAATATTTAATTTTAGGAAAAATTGTTTTAATTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFFF,FFF:FFFFFFF,FFFFFFFFF,FFFFFFFF:FFFFFFFF,FFFFFFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_7_R1.fq.gz_G_to_A.fastq and zr3534_7_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1723:1000_1:N:0:TTCCTACA+NGAATTCG/1 77 * 0 0 * * 0 0 TTTTCAATTAAAACAATTTTTCCTAAAATTACATATTATCTCATTTAATCCATCAATAAATAATATCATTTTTCAAAAAAAAAAATTTTTCCCAAAATCACATAATAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1723:1000_2:N:0:TTCCTACA+NGAATTCG/2 141 * 0 0 * * 0 0 TTTTAATTTTTATTATGTGATTTTGGGAAAAATTTTTTTTTTTGAAAAATTATATTATTTATTGATGGATTAAATGAGATAATATTTAATTTTAGGAAAAATTGTTTTAATTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFFF,FFF:FFFFFFF,FFFFFFFFF,FFFFFFFF:FFFFFFFF,FFFFFFFF,FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_7_R1.fq.gz_C_to_T.fastq and zr3534_7_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1723:1000_1:N:0:TTCCTACA+NGAATTCG/1 77 * 0 0 * * 0 0 TTTTTAATTAAAATAATTTTTTTTAAAATTATATATTATTTTATTTAATTTATTAATAAATAATATTATTTTTTAAAAAAAAAAATTTTTTTTAAAATTATATAATAAAAATTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF:FFFFFFFF:FFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1723:1000_2:N:0:TTCCTACA+NGAATTCG/2 141 * 0 0 * * 0 0 TTTTAATTTTTATTATATAATTTTAAAAAAAATTTTTTTTTTTAAAAAATTATATTATTTATTAATAAATTAAATAAAATAATATTTAATTTTAAAAAAAATTATTTTAATTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFF,FFFFFFFFFFFF,FFF:FFFFFFF,FFFFFFFFF,FFFFFFFF:FFFFFFFF,FFFFFFFF,FF YT:Z:UP >>> Writing bisulfite mapping results to zr3534_7_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73900 (73.90%) aligned concordantly 0 times 11770 (11.77%) aligned concordantly exactly 1 time 14330 (14.33%) aligned concordantly >1 times 26.10% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73422 (73.42%) aligned concordantly 0 times 12167 (12.17%) aligned concordantly exactly 1 time 14411 (14.41%) aligned concordantly >1 times 26.58% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73363 (73.36%) aligned concordantly 0 times 12252 (12.25%) aligned concordantly exactly 1 time 14385 (14.38%) aligned concordantly >1 times 26.64% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73560 (73.56%) aligned concordantly 0 times 11904 (11.90%) aligned concordantly exactly 1 time 14536 (14.54%) aligned concordantly >1 times 26.44% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_7_R1.fq.gz_C_to_T.fastq, zr3534_7_R1.fq.gz_G_to_A.fastq, zr3534_7_R2.fq.gz_C_to_T.fastq and zr3534_7_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61281 Mapping efficiency: 61.3% Sequence pairs with no alignments under any condition: 23002 Sequence pairs did not map uniquely: 15717 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15063 ((converted) top strand) GA/CT/CT: 15408 (complementary to (converted) top strand) GA/CT/GA: 15464 (complementary to (converted) bottom strand) CT/GA/GA: 15346 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2136176 Total methylated C's in CpG context: 28095 Total methylated C's in CHG context: 1704 Total methylated C's in CHH context: 7936 Total methylated C's in Unknown context: 89 Total unmethylated C's in CpG context: 244900 Total unmethylated C's in CHG context: 369082 Total unmethylated C's in CHH context: 1484459 Total unmethylated C's in Unknown context: 5394 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_8_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_8_R1.fq.gz Writing a C -> T converted version of the input file zr3534_8_R1.fq.gz to zr3534_8_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_8_R1.fq.gz to zr3534_8_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_8_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fq.gz Writing a C -> T converted version of the input file zr3534_8_R2.fq.gz to zr3534_8_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_8_R2.fq.gz to zr3534_8_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_8_R2.fq.gz (100001 sequences in total) Input files are zr3534_8_R1.fq.gz_C_to_T.fastq and zr3534_8_R1.fq.gz_G_to_A.fastq and zr3534_8_R2.fq.gz_C_to_T.fastq and zr3534_8_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_8_R1.fq.gz_C_to_T.fastq and zr3534_8_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1524:1000_1:N:0:ATCCAGGT+NCTGACGT/1 77 * 0 0 * * 0 0 TAATTTTTTTTTAATAAAATATATTTAATAATTTAAAATTTTTTATATTAAATTTTTATTATTATTATTTAAATTTATATAATAATTAAATTAAAATTTGATAATTAATAAAAT FFFFFFFF:F:FFFFFFF:FFF,FF:FFFFFFFFFFFFF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFF:,FFFFFFFF,FFFFFFFFF:F:,FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1524:1000_2:N:0:ATCCAGGT+NCTGACGT/2 141 * 0 0 * * 0 0 TTTTATTAAAATAATATTAAATTAATATATAAATTTTTATAAATTAATAATTTTATTATTATATAAAATTATATTAAATATTAATATTATTTTTATAATAATTAATTTTTTTTAA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_8_R1.fq.gz_G_to_A.fastq and zr3534_8_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1524:1000_1:N:0:ATCCAGGT+NCTGACGT/1 99 NC_047562.1_GA_converted 50728612 42 114M = 50728738 241 TAATTTTTTTCCAATAAAACATATCTAATAACTTAAAATCTTCTATATCAAATTTCCACCACTATTACTTAAACCTACATAACAATTAAATCAAAATTCAATAATCAACAAAAT FFFFFFFF:F:FFFFFFF:FFF,FF:FFFFFFFFFFFFF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFF:,FFFFFFFF,FFFFFFFFF:F:,FF AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:59T17T36 YS:i:-6 YT:Z:CP A00742:163:HLTJMDSXY:1:1101:1524:1000_2:N:0:ATCCAGGT+NCTGACGT/2 147 NC_047562.1_GA_converted 50728738 42 115M = 50728612 -241 CTAAAAAAAATCAATTACTACAAAAATAATACCAATATCTAACATAATTCCATATAACAATAAAATTATCAATTTACAAAAACCTACATATCAACCTAACATTACCTCAATAAAA :FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:17A97 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_8_R1.fq.gz_G_to_A.fastq and zr3534_8_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1524:1000_1:N:0:ATCCAGGT+NCTGACGT/1 77 * 0 0 * * 0 0 TAATTTTTTTCCAATAAAACATATCTAATAACTTAAAATCTTCTATATCAAATTTCCACCACTATTACTTAAACCTACATAACAATTAAATCAAAATTCAATAATCAACAAAAT FFFFFFFF:F:FFFFFFF:FFF,FF:FFFFFFFFFFFFF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFF:,FFFFFFFF,FFFFFFFFF:F:,FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1524:1000_2:N:0:ATCCAGGT+NCTGACGT/2 141 * 0 0 * * 0 0 TTTTATTGAGGTAATGTTAGGTTGATATGTAGGTTTTTGTAAATTGATAATTTTATTGTTATATGGAATTATGTTAGATATTGGTATTATTTTTGTAGTAATTGATTTTTTTTAG FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_8_R1.fq.gz_C_to_T.fastq and zr3534_8_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:1524:1000_1:N:0:ATCCAGGT+NCTGACGT/1 77 * 0 0 * * 0 0 TAATTTTTTTTTAATAAAATATATTTAATAATTTAAAATTTTTTATATTAAATTTTTATTATTATTATTTAAATTTATATAATAATTAAATTAAAATTTGATAATTAATAAAAT FFFFFFFF:F:FFFFFFF:FFF,FF:FFFFFFFFFFFFF:FF:FFFF:FFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFFFFF:FFFF:,FFFFFFFF,FFFFFFFFF:F:,FF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:1524:1000_2:N:0:ATCCAGGT+NCTGACGT/2 141 * 0 0 * * 0 0 TTTTATTAAAATAATATTAAATTAATATATAAATTTTTATAAATTAATAATTTTATTATTATATAAAATTATATTAAATATTAATATTATTTTTATAATAATTAATTTTTTTTAA FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP >>> Writing bisulfite mapping results to zr3534_8_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72805 (72.81%) aligned concordantly 0 times 12333 (12.33%) aligned concordantly exactly 1 time 14862 (14.86%) aligned concordantly >1 times 27.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73026 (73.03%) aligned concordantly 0 times 12243 (12.24%) aligned concordantly exactly 1 time 14731 (14.73%) aligned concordantly >1 times 26.97% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73189 (73.19%) aligned concordantly 0 times 12062 (12.06%) aligned concordantly exactly 1 time 14749 (14.75%) aligned concordantly >1 times 26.81% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73310 (73.31%) aligned concordantly 0 times 12019 (12.02%) aligned concordantly exactly 1 time 14671 (14.67%) aligned concordantly >1 times 26.69% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_8_R1.fq.gz_C_to_T.fastq, zr3534_8_R1.fq.gz_G_to_A.fastq, zr3534_8_R2.fq.gz_C_to_T.fastq and zr3534_8_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61749 Mapping efficiency: 61.7% Sequence pairs with no alignments under any condition: 21889 Sequence pairs did not map uniquely: 16362 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15222 ((converted) top strand) GA/CT/CT: 15485 (complementary to (converted) top strand) GA/CT/GA: 15661 (complementary to (converted) bottom strand) CT/GA/GA: 15381 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2134624 Total methylated C's in CpG context: 28579 Total methylated C's in CHG context: 1697 Total methylated C's in CHH context: 7682 Total methylated C's in Unknown context: 75 Total unmethylated C's in CpG context: 246032 Total unmethylated C's in CHG context: 369826 Total unmethylated C's in CHH context: 1480808 Total unmethylated C's in Unknown context: 5344 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3534_9_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3534_9_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_9_R1.fq.gz Writing a C -> T converted version of the input file zr3534_9_R1.fq.gz to zr3534_9_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_9_R1.fq.gz to zr3534_9_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_9_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fq.gz Writing a C -> T converted version of the input file zr3534_9_R2.fq.gz to zr3534_9_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3534_9_R2.fq.gz to zr3534_9_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3534_9_R2.fq.gz (100001 sequences in total) Input files are zr3534_9_R1.fq.gz_C_to_T.fastq and zr3534_9_R1.fq.gz_G_to_A.fastq and zr3534_9_R2.fq.gz_C_to_T.fastq and zr3534_9_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3534_9_R1.fq.gz_C_to_T.fastq and zr3534_9_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:2193:1000_1:N:0:CTTATTGG+NCTTGTTA/1 77 * 0 0 * * 0 0 TGGTATTATTTAAAGTTTTGGGGGTATGTTTGTGGATTGTGGATGTTTTGTTTATTTGTAGGATGTTGTTTTTTGGATGTGTTAGTTTTTTAGTTTTAGTAAAAAAGATAATTTT FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:2193:1000_2:N:0:CTTATTGG+NCTTGTTA/2 141 * 0 0 * * 0 0 TTATTAAAAATTATCTTTTTTACTAAAACTAAAAAACTAACACATCCAAAAAACAACATCCTACAAATAAACAAAACATCCACAATCCACAAACATACCCCCAAAACTTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF,FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3534_9_R1.fq.gz_G_to_A.fastq and zr3534_9_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:2193:1000_1:N:0:CTTATTGG+NCTTGTTA/1 77 * 0 0 * * 0 0 TAATATTATTTAAAATTTTAAAAATATATTTATAAATTATAAATATTTTATTTATTTATAAAATATTATTTTTTAAATATATTAATTTTTTAATTTCAATAAAAAAAATAATTTT FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:2193:1000_2:N:0:CTTATTGG+NCTTGTTA/2 141 * 0 0 * * 0 0 TTATTAAAAATTATTTTTTTTATTGAAATTAAAAAATTAATATATTTAAAAAATAATATTTTATAAATAAATAAAATATTTATAATTTATAAATATATTTTTAAAATTTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF,FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3534_9_R1.fq.gz_G_to_A.fastq and zr3534_9_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:2193:1000_1:N:0:CTTATTGG+NCTTGTTA/1 77 * 0 0 * * 0 0 TAATATTATTTAAAATTTTAAAAATATATTTATAAATTATAAATATTTTATTTATTTATAAAATATTATTTTTTAAATATATTAATTTTTTAATTTCAATAAAAAAAATAATTTT FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:2193:1000_2:N:0:CTTATTGG+NCTTGTTA/2 141 * 0 0 * * 0 0 TTATTAAAAATTATTTTTTTTATTGAAATTAAAAAATTAATATATTTAAAAAATAATATTTTATAAATAAATAAAATATTTATAATTTATAAATATATTTTTAAAATTTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF,FFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3534_9_R1.fq.gz_C_to_T.fastq and zr3534_9_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:163:HLTJMDSXY:1:1101:2193:1000_1:N:0:CTTATTGG+NCTTGTTA/1 77 * 0 0 * * 0 0 TGGTATTATTTAAAGTTTTGGGGGTATGTTTGTGGATTGTGGATGTTTTGTTTATTTGTAGGATGTTGTTTTTTGGATGTGTTAGTTTTTTAGTTTTAGTAAAAAAGATAATTTT FFFFF:FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF YT:Z:UP A00742:163:HLTJMDSXY:1:1101:2193:1000_2:N:0:CTTATTGG+NCTTGTTA/2 141 * 0 0 * * 0 0 TTATTAAAAATTATCTTTTTTACTAAAACTAAAAAACTAACACATCCAAAAAACAACATCCTACAAATAAACAAAACATCCACAATCCACAAACATACCCCCAAAACTTTAAATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFF,FFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3534_9_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3534_9_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fq.gz Chromosomal sequence could not be extracted for A00742:163:HLTJMDSXY:1:1101:12671:33426_1:N:0:CTTATTGG+ACTTGTTA NW_022994786.1 1 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (72932 (72.93%) aligned concordantly 0 times100.00 % ) were paired; of these:12178 ( 12.1872827% () aligned concordantly exactly 1 time72.83 % ) aligned concordantly 0 times14890 ( 14.8912286% () aligned concordantly >1 times12.29 %27.07) aligned concordantly exactly 1 time% overall alignment rate 14887 (14.89%) aligned concordantly >1 times 27.17% overall alignment rate 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00100.00%%) were paired; of these:) were paired; of these: 7288072879 ( (72.8872.88%%) aligned concordantly 0 times) aligned concordantly 0 times 1207412263 ( (12.0712.26%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 1504614858 ( (15.0514.86%%) aligned concordantly >1 times) aligned concordantly >1 times 27.1227.12%% overall alignment rate overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3534_9_R1.fq.gz_C_to_T.fastq, zr3534_9_R1.fq.gz_G_to_A.fastq, zr3534_9_R2.fq.gz_C_to_T.fastq and zr3534_9_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61885 Mapping efficiency: 61.9% Sequence pairs with no alignments under any condition: 21378 Sequence pairs did not map uniquely: 16737 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15407 ((converted) top strand) GA/CT/CT: 15476 (complementary to (converted) top strand) GA/CT/GA: 15624 (complementary to (converted) bottom strand) CT/GA/GA: 15377 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2175764 Total methylated C's in CpG context: 28518 Total methylated C's in CHG context: 1819 Total methylated C's in CHH context: 7613 Total methylated C's in Unknown context: 87 Total unmethylated C's in CpG context: 256743 Total unmethylated C's in CHG context: 382839 Total unmethylated C's in CHH context: 1498232 Total unmethylated C's in Unknown context: 5430 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_10_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_10_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_10_R1.fq.gz Writing a C -> T converted version of the input file zr3644_10_R1.fq.gz to zr3644_10_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_10_R1.fq.gz to zr3644_10_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_10_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fq.gz Writing a C -> T converted version of the input file zr3644_10_R2.fq.gz to zr3644_10_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_10_R2.fq.gz to zr3644_10_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_10_R2.fq.gz (100001 sequences in total) Input files are zr3644_10_R1.fq.gz_C_to_T.fastq and zr3644_10_R1.fq.gz_G_to_A.fastq and zr3644_10_R2.fq.gz_C_to_T.fastq and zr3644_10_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_10_R1.fq.gz_C_to_T.fastq and zr3644_10_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5412:1000_1:N:0:NCCGTTAC+TCGCTATG/1 77 * 0 0 * * 0 0 AATAAAATTTAAATTATTTATTAAATAATATTATTATATTATATTTATTAAAAATTTATAAAAAAATAAAAAAAATTAAAAAAATTTTTAATAATATTATAATAAATTAAATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFF:FFF,F:FFFFFFFF:FFFFFFFFFF:FFFF,FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5412:1000_2:N:0:NCCGTTAC+TCGCTATG/2 141 * 0 0 * * 0 0 TTTTTATATATATTTTATATATAAATTTTTTATATATAATTTAAATTAATAAATATATATTATTAATTAAATTATTAAATTATATATTATAAATTTAATTTATTATAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF,F:FF:FFFFF:F:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_10_R1.fq.gz_G_to_A.fastq and zr3644_10_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5412:1000_1:N:0:NCCGTTAC+TCGCTATG/1 99 NC_047567.1_GA_converted 10679673 40 115M = 10679762 204 AATAAAACTCAAATTATTCACTAAATAACACCACCACATCACATCTACCAAAAATTTATAAAAAAACAAAAAAAACCAAAAAAATCTTTAATAATACCACAACAAATCAAATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFF:FFF,F:FFFFFFFF:FFFFFFFFFF:FFFF,FF AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:9T73C31 YS:i:-24 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:5412:1000_2:N:0:NCCGTTAC+TCGCTATG/2 147 NC_047567.1_GA_converted 10679762 40 115M = 10679673 -204 AATAATACCACAACAAATCAAATTTATAACATATAATTTAATAATTCAACCAATAACACATATTTACTAATTTAAATCACACATAAAAAACTTACATATAAAACATATATAAAAA FFFFF:F:FFFFF:FF:F,FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:66T6T17A13A9 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_10_R1.fq.gz_G_to_A.fastq and zr3644_10_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5412:1000_1:N:0:NCCGTTAC+TCGCTATG/1 77 * 0 0 * * 0 0 AATAAAACTCAAATTATTCACTAAATAACACCACCACATCACATCTACCAAAAATTTATAAAAAAACAAAAAAAACCAAAAAAATCTTTAATAATACCACAACAAATCAAATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFF:FFF,F:FFFFFFFF:FFFFFFFFFF:FFFF,FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5412:1000_2:N:0:NCCGTTAC+TCGCTATG/2 141 * 0 0 * * 0 0 TTTTTATATATGTTTTATATGTAAGTTTTTTATGTGTGATTTAAATTAGTAAATATGTGTTATTGGTTGAATTATTAAATTATATGTTATAAATTTGATTTGTTGTGGTATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF,F:FF:FFFFF:F:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_10_R1.fq.gz_C_to_T.fastq and zr3644_10_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5412:1000_1:N:0:NCCGTTAC+TCGCTATG/1 77 * 0 0 * * 0 0 AATAAAATTTAAATTATTTATTAAATAATATTATTATATTATATTTATTAAAAATTTATAAAAAAATAAAAAAAATTAAAAAAATTTTTAATAATATTATAATAAATTAAATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFF:FFF,F:FFFFFFFF:FFFFFFFFFF:FFFF,FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5412:1000_2:N:0:NCCGTTAC+TCGCTATG/2 141 * 0 0 * * 0 0 TTTTTATATATATTTTATATATAAATTTTTTATATATAATTTAAATTAATAAATATATATTATTAATTAAATTATTAAATTATATATTATAAATTTAATTTATTATAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF,F:FF:FFFFF:F:FFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_10_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_10_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:6352:13150_1:N:0:ACCGTTAC+TCGCTATG NW_022994911.1 1 100000 reads; of these: 100000 (100.00%) were paired; of these: 72984 (72.98%) aligned concordantly 0 times 11933 (11.93%) aligned concordantly exactly 1 time 15083 (15.08%) aligned concordantly >1 times 27.02% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72996 (73.00%) aligned concordantly 0 times 12088 (12.09%100000) aligned concordantly exactly 1 time reads; of these: 14916100000 ( (14.92%) aligned concordantly >1 times 27.00100.00%% overall alignment rate) were paired; of these: 72903 (72.90%) aligned concordantly 0 times 12144 (12.14%) aligned concordantly exactly 1 time 14953 (14.95%) aligned concordantly >1 times 27.10% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72741 (72.74%) aligned concordantly 0 times 12209 (12.21%) aligned concordantly exactly 1 time 15050 (15.05%) aligned concordantly >1 times 27.26% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_10_R1.fq.gz_C_to_T.fastq, zr3644_10_R1.fq.gz_G_to_A.fastq, zr3644_10_R2.fq.gz_C_to_T.fastq and zr3644_10_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61154 Mapping efficiency: 61.2% Sequence pairs with no alignments under any condition: 21890 Sequence pairs did not map uniquely: 16956 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15210 ((converted) top strand) GA/CT/CT: 15214 (complementary to (converted) top strand) GA/CT/GA: 15355 (complementary to (converted) bottom strand) CT/GA/GA: 15374 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2154179 Total methylated C's in CpG context: 29648 Total methylated C's in CHG context: 1760 Total methylated C's in CHH context: 7608 Total methylated C's in Unknown context: 68 Total unmethylated C's in CpG context: 251436 Total unmethylated C's in CHG context: 375780 Total unmethylated C's in CHH context: 1487947 Total unmethylated C's in Unknown context: 5343 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_11_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_11_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_11_R1.fq.gz Writing a C -> T converted version of the input file zr3644_11_R1.fq.gz to zr3644_11_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_11_R1.fq.gz to zr3644_11_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_11_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fq.gz Writing a C -> T converted version of the input file zr3644_11_R2.fq.gz to zr3644_11_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_11_R2.fq.gz to zr3644_11_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_11_R2.fq.gz (100001 sequences in total) Input files are zr3644_11_R1.fq.gz_C_to_T.fastq and zr3644_11_R1.fq.gz_G_to_A.fastq and zr3644_11_R2.fq.gz_C_to_T.fastq and zr3644_11_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_11_R1.fq.gz_C_to_T.fastq and zr3644_11_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1542:1000_1:N:0:NATGCCTT+TAATGTGT/1 77 * 0 0 * * 0 0 ATGTAAAAATTAAAAAAATTATTAATTTATTTTAATTAAATTTAAATTTTAAAATTTTAATTTTTTTATTTTAAAATTTAAATTAAAAAATATATTTATGAATTATTATATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFF,F:,,,F:F:F:FFF,::FF:FFF:FFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1542:1000_2:N:0:NATGCCTT+TAATGTGT/2 141 * 0 0 * * 0 0 TTAAAATTAAATAAAATATTTTTTAATTAATATAATAATTCATAAATATATTTTTTAATTTAAATTTTAAAATAAAAAAATTAAAATTTTAAAATTTAAATTTAATTAAAATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_11_R1.fq.gz_G_to_A.fastq and zr3644_11_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1542:1000_1:N:0:NATGCCTT+TAATGTGT/1 77 * 0 0 * * 0 0 ACATAAAAATTAAAAAAACTATTAATTCATTCTAATTAAATTCAAATTCCAAAATTTTAACTTTTTTATTTTAAAATTTAAATTAAAAAACACATCCACAAACTACTATACCAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFF,F:,,,F:F:F:FFF,::FF:FFF:FFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1542:1000_2:N:0:NATGCCTT+TAATGTGT/2 141 * 0 0 * * 0 0 TTGAAGTTAAGTAGAATATTTTTTGGTTGGTATAGTAGTTTGTGGATGTGTTTTTTAATTTAAATTTTAAAATAAAAAAGTTAAAATTTTGGAATTTGAATTTAATTAGAATGAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_11_R1.fq.gz_G_to_A.fastq and zr3644_11_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1542:1000_1:N:0:NATGCCTT+TAATGTGT/1 83 NC_047562.1_CT_converted 32907628 40 48M1D67M = 32907603 -141 GTTGGTATAGTAGTTTGTGGATGTGTTTTTTAATTTAAATTTTAAAATAAAAAAGTTAAAATTTTGGAATTTGAATTTAATTAGAATGAATTAATAGTTTTTTTAATTTTTATGT F,FFF:FFF:FF::,FFF:F:F:F,,,:F,FFF:FFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:16T31^A67 YS:i:-14 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1542:1000_2:N:0:NATGCCTT+TAATGTGT/2 163 NC_047562.1_CT_converted 32907603 40 73M1D42M = 32907628 141 TTGAAGTTAAGTAGAATATTTTTTGGTTGGTATAGTAGTTTGTGGATGTGTTTTTTAATTTAAATTTTAAAATAAAAAAGTTAAAATTTTGGAATTTGAATTTAATTAGAATGAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFF:FF AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:41T31^A42 YS:i:-14 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_11_R1.fq.gz_C_to_T.fastq and zr3644_11_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1542:1000_1:N:0:NATGCCTT+TAATGTGT/1 77 * 0 0 * * 0 0 ATGTAAAAATTAAAAAAATTATTAATTTATTTTAATTAAATTTAAATTTTAAAATTTTAATTTTTTTATTTTAAAATTTAAATTAAAAAATATATTTATGAATTATTATATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFF,F:,,,F:F:F:FFF,::FF:FFF:FFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1542:1000_2:N:0:NATGCCTT+TAATGTGT/2 141 * 0 0 * * 0 0 TTAAAATTAAATAAAATATTTTTTAATTAATATAATAATTCATAAATATATTTTTTAATTTAAATTTTAAAATAAAAAAATTAAAATTTTAAAATTTAAATTTAATTAAAATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFF:FF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_11_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_11_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1101:5276:34303_1:N:0:TATGCCTT+TAATGTGT NC_001276.1 18122 100000 reads; of these: 100000 (100.00%) were paired; of these: 72809 (72.81%) aligned concordantly 0 times 12152 (12.15%) aligned concordantly exactly 1 time 15039 (15.04%) aligned concordantly >1 times 27.19% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72923 (72.92%) aligned concordantly 0 times 12085 (12.09%) aligned concordantly exactly 1 time 14992 (14.99%) aligned concordantly >1 times 27.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72978 (72.98%) aligned concordantly 0 times 12036 (12.04%) aligned concordantly exactly 1 time 14986 (14.99%) aligned concordantly >1 times 27.02% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72976 (72.98%) aligned concordantly 0 times 12011 (12.01%) aligned concordantly exactly 1 time 15013 (15.01%) aligned concordantly >1 times 27.02% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_11_R1.fq.gz_C_to_T.fastq, zr3644_11_R1.fq.gz_G_to_A.fastq, zr3644_11_R2.fq.gz_C_to_T.fastq and zr3644_11_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60961 Mapping efficiency: 61.0% Sequence pairs with no alignments under any condition: 21931 Sequence pairs did not map uniquely: 17108 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15225 ((converted) top strand) GA/CT/CT: 15162 (complementary to (converted) top strand) GA/CT/GA: 15415 (complementary to (converted) bottom strand) CT/GA/GA: 15158 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2144161 Total methylated C's in CpG context: 28507 Total methylated C's in CHG context: 1764 Total methylated C's in CHH context: 7966 Total methylated C's in Unknown context: 80 Total unmethylated C's in CpG context: 250610 Total unmethylated C's in CHG context: 374259 Total unmethylated C's in CHH context: 1481055 Total unmethylated C's in Unknown context: 5438 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_12_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_12_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_12_R1.fq.gz Writing a C -> T converted version of the input file zr3644_12_R1.fq.gz to zr3644_12_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_12_R1.fq.gz to zr3644_12_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_12_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fq.gz Writing a C -> T converted version of the input file zr3644_12_R2.fq.gz to zr3644_12_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_12_R2.fq.gz to zr3644_12_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_12_R2.fq.gz (100001 sequences in total) Input files are zr3644_12_R1.fq.gz_C_to_T.fastq and zr3644_12_R1.fq.gz_G_to_A.fastq and zr3644_12_R2.fq.gz_C_to_T.fastq and zr3644_12_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_12_R1.fq.gz_C_to_T.fastq and zr3644_12_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3134:1000_1:N:0:NCAAGTGG+AACATCGC/1 77 * 0 0 * * 0 0 GTTTAAGAGAAGTTTTAGGGAATAAAGAAAGGATAATTTATTAATTTTAATGTTATATATATTTATTTAAGAAATATT FFFFF:F:F:FFFFFFFFFFFFF:F:FF,FFF,F,,FFFFFFF:FFFF:,FFFF:F,FFFFFFF,FFFF,:,:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3134:1000_2:N:0:NCAAGTGG+AACATCGC/2 141 * 0 0 * * 0 0 AAATAAATATATATAACATTAAAATTAATAAATTATCCTTTCTTTATTCCCTAAAACTTCTCTTAAACATTTTTATAT FF:FFFFFFFFFFF:FFFFFFFFFFFF:FF:,FF,F,,FFF:FFF,FFFF:FF::,,FF,F:FF::,,:FFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_12_R1.fq.gz_G_to_A.fastq and zr3644_12_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3134:1000_1:N:0:NCAAGTGG+AACATCGC/1 77 * 0 0 * * 0 0 ATTTAAAAAAAATTTTAAAAAATAAAAAAAAAATAATTTATTAATTTTAATATTATATATATTTATTTAAAAAATATT FFFFF:F:F:FFFFFFFFFFFFF:F:FF,FFF,F,,FFFFFFF:FFFF:,FFFF:F,FFFFFFF,FFFF,:,:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3134:1000_2:N:0:NCAAGTGG+AACATCGC/2 141 * 0 0 * * 0 0 AAATAAATATATATAATATTAAAATTAATAAATTATTTTTTTTTTATTTTTTAAAATTTTTTTTAAATATTTTTATAT FF:FFFFFFFFFFF:FFFFFFFFFFFF:FF:,FF,F,,FFF:FFF,FFFF:FF::,,FF,F:FF::,,:FFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_12_R1.fq.gz_G_to_A.fastq and zr3644_12_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3134:1000_1:N:0:NCAAGTGG+AACATCGC/1 77 * 0 0 * * 0 0 ATTTAAAAAAAATTTTAAAAAATAAAAAAAAAATAATTTATTAATTTTAATATTATATATATTTATTTAAAAAATATT FFFFF:F:F:FFFFFFFFFFFFF:F:FF,FFF,F,,FFFFFFF:FFFF:,FFFF:F,FFFFFFF,FFFF,:,:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3134:1000_2:N:0:NCAAGTGG+AACATCGC/2 141 * 0 0 * * 0 0 AAATAAATATATATAATATTAAAATTAATAAATTATTTTTTTTTTATTTTTTAAAATTTTTTTTAAATATTTTTATAT FF:FFFFFFFFFFF:FFFFFFFFFFFF:FF:,FF,F,,FFF:FFF,FFFF:FF::,,FF,F:FF::,,:FFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_12_R1.fq.gz_C_to_T.fastq and zr3644_12_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3134:1000_1:N:0:NCAAGTGG+AACATCGC/1 83 NC_047564.1_GA_converted 58462001 3 78M = 58462011 88 AATATTTCTTAAATAAATATATATAACATTAAAATTAATAAATTATCCTTTCTTTATTCCCTAAAACTTCTCTTAAAC FF:FF:,:,FFFF,FFFFFFF,F:FFFF,:FFFF:FFFFFFF,,F,FFF,FF:F:FFFFFFFFFFFFF:F:F:FFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:2C37T11A6T9A8 YS:i:-30 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:3134:1000_2:N:0:NCAAGTGG+AACATCGC/2 163 NC_047564.1_GA_converted 58462011 3 78M = 58462001 -88 AAATAAATATATATAACATTAAAATTAATAAATTATCCTTTCTTTATTCCCTAAAACTTCTCTTAAACATTTTTATAT FF:FFFFFFFFFFF:FFFFFFFFFFFF:FF:,FF,F,,FFF:FFF,FFFF:FF::,,FF,F:FF::,,:FFFFFFF:F AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:30T11A6T9A12C5 YS:i:-30 YT:Z:CP >>> Writing bisulfite mapping results to zr3644_12_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_12_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fq.gz 100000 reads; of these:100000 reads; of these: 100000 (100000 (100.00%) were paired; of these: 72844 (72.84100.00%%) aligned concordantly 0 times) were paired; of these: 1207373187 ( (12.0773.19%%100000) aligned concordantly exactly 1 time) aligned concordantly 0 times reads; of these: 1508311868100000 ( ( (15.0811.87%%) aligned concordantly >1 times100.00) aligned concordantly exactly 1 time % 27.16) were paired; of these: % 14945 overall alignment rate ( 7303814.95 (%73.04) aligned concordantly >1 times% ) aligned concordantly 0 times26.81 % overall alignment rate12041 (12.04%) aligned concordantly exactly 1 time 14921 (14.92%) aligned concordantly >1 times 26.96% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72932 (72.93%) aligned concordantly 0 times 12014 (12.01%) aligned concordantly exactly 1 time 15054 (15.05%) aligned concordantly >1 times 27.07% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_12_R1.fq.gz_C_to_T.fastq, zr3644_12_R1.fq.gz_G_to_A.fastq, zr3644_12_R2.fq.gz_C_to_T.fastq and zr3644_12_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61367 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 22024 Sequence pairs did not map uniquely: 16609 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15356 ((converted) top strand) GA/CT/CT: 15506 (complementary to (converted) top strand) GA/CT/GA: 15379 (complementary to (converted) bottom strand) CT/GA/GA: 15126 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2130237 Total methylated C's in CpG context: 26218 Total methylated C's in CHG context: 1646 Total methylated C's in CHH context: 7156 Total methylated C's in Unknown context: 62 Total unmethylated C's in CpG context: 241599 Total unmethylated C's in CHG context: 358327 Total unmethylated C's in CHH context: 1495291 Total unmethylated C's in Unknown context: 5307 C methylated in CpG context: 9.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.2% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_13_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_13_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_13_R1.fq.gz Writing a C -> T converted version of the input file zr3644_13_R1.fq.gz to zr3644_13_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_13_R1.fq.gz to zr3644_13_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_13_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fq.gz Writing a C -> T converted version of the input file zr3644_13_R2.fq.gz to zr3644_13_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_13_R2.fq.gz to zr3644_13_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_13_R2.fq.gz (100001 sequences in total) Input files are zr3644_13_R1.fq.gz_C_to_T.fastq and zr3644_13_R1.fq.gz_G_to_A.fastq and zr3644_13_R2.fq.gz_C_to_T.fastq and zr3644_13_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_13_R1.fq.gz_C_to_T.fastq and zr3644_13_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:21025:1611_1:N:0:TGGTACCT+AGTACTCA/1 77 * 0 0 * * 0 0 AATTTTTATTTATGTAAAAAAAAAAAATAAGTTTTTAATTTTAAATTATTTGTTATTTTTTTTATTTAATATATTGAGAGAGAAATTTTGGTTGTGTGTTTTGATAATATTTTAT FF:FFF:F:FFFFFFFFFFFF:F:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FF:F:FF::F,FFF,F:FFF,FFF,FF:FFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:21025:1611_2:N:0:TGGTACCT+AGTACTCA/2 141 * 0 0 * * 0 0 ACTTTAAAAATAACACCCATTTAATATCATACAATAAAATATTATCAAAACACAAAACCAAAATTTCTCTCTCAATATATTAAATAAAAAAAATAACAAATAATTTAAAATTAAA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_13_R1.fq.gz_G_to_A.fastq and zr3644_13_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:21025:1611_1:N:0:TGGTACCT+AGTACTCA/1 77 * 0 0 * * 0 0 AATTTTTATTTATATAAAAAAAAAAAATAAATTTTTAATTTTAAATTATTTATTATTTTTTTTATTTAATATATTAAAAAAAAAATTTTAATTATATATTTTAATAATATTTTAT FF:FFF:F:FFFFFFFFFFFF:F:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FF:F:FF::F,FFF,F:FFF,FFF,FF:FFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:21025:1611_2:N:0:TGGTACCT+AGTACTCA/2 141 * 0 0 * * 0 0 ATTTTAAAAATAATATTTATTTAATATTATATAATAAAATATTATTAAAATATAAAATTAAAATTTTTTTTTTAATATATTAAATAAAAAAAATAATAAATAATTTAAAATTAAA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_13_R1.fq.gz_G_to_A.fastq and zr3644_13_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:21025:1611_1:N:0:TGGTACCT+AGTACTCA/1 77 * 0 0 * * 0 0 AATTTTTATTTATATAAAAAAAAAAAATAAATTTTTAATTTTAAATTATTTATTATTTTTTTTATTTAATATATTAAAAAAAAAATTTTAATTATATATTTTAATAATATTTTAT FF:FFF:F:FFFFFFFFFFFF:F:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FF:F:FF::F,FFF,F:FFF,FFF,FF:FFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:21025:1611_2:N:0:TGGTACCT+AGTACTCA/2 141 * 0 0 * * 0 0 ATTTTAAAAATAATATTTATTTAATATTATATAATAAAATATTATTAAAATATAAAATTAAAATTTTTTTTTTAATATATTAAATAAAAAAAATAATAAATAATTTAAAATTAAA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_13_R1.fq.gz_C_to_T.fastq and zr3644_13_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:21025:1611_1:N:0:TGGTACCT+AGTACTCA/1 77 * 0 0 * * 0 0 AATTTTTATTTATGTAAAAAAAAAAAATAAGTTTTTAATTTTAAATTATTTGTTATTTTTTTTATTTAATATATTGAGAGAGAAATTTTGGTTGTGTGTTTTGATAATATTTTAT FF:FFF:F:FFFFFFFFFFFF:F:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F:FFFFFFF:FF:F:FF::F,FFF,F:FFF,FFF,FF:FFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:21025:1611_2:N:0:TGGTACCT+AGTACTCA/2 141 * 0 0 * * 0 0 ACTTTAAAAATAACACCCATTTAATATCATACAATAAAATATTATCAAAACACAAAACCAAAATTTCTCTCTCAATATATTAAATAAAAAAAATAACAAATAATTTAAAATTAAA FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_13_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_13_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72988 (72.99%) aligned concordantly 0 times 12266 (12.27%) aligned concordantly exactly 1 time 14746 (14.75%) aligned concordantly >1 times 27.01% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73041 (73.04%) aligned concordantly 0 times 12096 (12.10%) aligned concordantly exactly 1 time 14863 (14.86%) aligned concordantly >1 times 26.96% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73102 (73.10%) aligned concordantly 0 times 12116 (12.12%) aligned concordantly exactly 1 time 14782 (14.78%) aligned concordantly >1 times 26.90% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73062 (73.06%) aligned concordantly 0 times 12124 (12.12%) aligned concordantly exactly 1 time 14814 (14.81%) aligned concordantly >1 times 26.94% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_13_R1.fq.gz_C_to_T.fastq, zr3644_13_R1.fq.gz_G_to_A.fastq, zr3644_13_R2.fq.gz_C_to_T.fastq and zr3644_13_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61792 Mapping efficiency: 61.8% Sequence pairs with no alignments under any condition: 21880 Sequence pairs did not map uniquely: 16328 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15417 ((converted) top strand) GA/CT/CT: 15456 (complementary to (converted) top strand) GA/CT/GA: 15454 (complementary to (converted) bottom strand) CT/GA/GA: 15465 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2186112 Total methylated C's in CpG context: 28902 Total methylated C's in CHG context: 1781 Total methylated C's in CHH context: 7859 Total methylated C's in Unknown context: 89 Total unmethylated C's in CpG context: 251857 Total unmethylated C's in CHG context: 378544 Total unmethylated C's in CHH context: 1517169 Total unmethylated C's in Unknown context: 5394 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fq.gz Writing a C -> T converted version of the input file zr3644_14_R1.fq.gz to zr3644_14_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_14_R1.fq.gz to zr3644_14_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_14_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fq.gz Writing a C -> T converted version of the input file zr3644_14_R2.fq.gz to zr3644_14_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_14_R2.fq.gz to zr3644_14_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_14_R2.fq.gz (100001 sequences in total) Input files are zr3644_14_R1.fq.gz_C_to_T.fastq and zr3644_14_R1.fq.gz_G_to_A.fastq and zr3644_14_R2.fq.gz_C_to_T.fastq and zr3644_14_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_14_R1.fq.gz_C_to_T.fastq and zr3644_14_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2374:1000_1:N:0:NTGGAATT+GTATTGAC/1 77 * 0 0 * * 0 0 TTAAATAAAAAAAATATTATTTTAAATGTGT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2374:1000_2:N:0:NTGGAATT+GTATTGAC/2 141 * 0 0 * * 0 0 TATTTTTTTTATTTAAAAAATATAATATTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_14_R1.fq.gz_G_to_A.fastq and zr3644_14_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2374:1000_1:N:0:NTGGAATT+GTATTGAC/1 77 * 0 0 * * 0 0 CTAAACAAAAAAAACATCACTTTAAACACAT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2374:1000_2:N:0:NTGGAATT+GTATTGAC/2 141 * 0 0 * * 0 0 TGTTTTTTTTGTTTAGAGAATGTAATGTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_14_R1.fq.gz_G_to_A.fastq and zr3644_14_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2374:1000_1:N:0:NTGGAATT+GTATTGAC/1 77 * 0 0 * * 0 0 CTAAACAAAAAAAACATCACTTTAAACACAT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2374:1000_2:N:0:NTGGAATT+GTATTGAC/2 141 * 0 0 * * 0 0 TGTTTTTTTTGTTTAGAGAATGTAATGTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_14_R1.fq.gz_C_to_T.fastq and zr3644_14_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2374:1000_1:N:0:NTGGAATT+GTATTGAC/1 77 * 0 0 * * 0 0 TTAAATAAAAAAAATATTATTTTAAATGTGT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2374:1000_2:N:0:NTGGAATT+GTATTGAC/2 141 * 0 0 * * 0 0 TATTTTTTTTATTTAAAAAATATAATATTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_14_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1101:27019:5509_1:N:0:TTGGAATT+GTATTGAC NC_001276.1 18117 100000 reads; of these: 100000 (100.00%) were paired; of these: 72583 (72.58%) aligned concordantly 0 times 12410 (12.41%) aligned concordantly exactly 1 time 15007 (15.01%) aligned concordantly >1 times 27.42% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72790 (72.79%) aligned concordantly 0 times 12261 (12.26%) aligned concordantly exactly 1 time 14949 (14.95%) aligned concordantly >1 times 27.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73264 (73.26%) aligned concordantly 0 times 11897 (11.90%) aligned concordantly exactly 1 time 14839 (14.84%) aligned concordantly >1 times 26.74% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73096 (73.10%) aligned concordantly 0 times 12243 (12.24%) aligned concordantly exactly 1 time 14661 (14.66%) aligned concordantly >1 times 26.90% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_14_R1.fq.gz_C_to_T.fastq, zr3644_14_R1.fq.gz_G_to_A.fastq, zr3644_14_R2.fq.gz_C_to_T.fastq and zr3644_14_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 62089 Mapping efficiency: 62.1% Sequence pairs with no alignments under any condition: 21390 Sequence pairs did not map uniquely: 16521 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15451 ((converted) top strand) GA/CT/CT: 15505 (complementary to (converted) top strand) GA/CT/GA: 15794 (complementary to (converted) bottom strand) CT/GA/GA: 15338 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2178029 Total methylated C's in CpG context: 32720 Total methylated C's in CHG context: 1899 Total methylated C's in CHH context: 7658 Total methylated C's in Unknown context: 85 Total unmethylated C's in CpG context: 246804 Total unmethylated C's in CHG context: 376144 Total unmethylated C's in CHH context: 1512804 Total unmethylated C's in Unknown context: 5234 C methylated in CpG context: 11.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_15_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_15_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_15_R1.fq.gz Writing a C -> T converted version of the input file zr3644_15_R1.fq.gz to zr3644_15_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_15_R1.fq.gz to zr3644_15_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_15_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fq.gz Writing a C -> T converted version of the input file zr3644_15_R2.fq.gz to zr3644_15_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_15_R2.fq.gz to zr3644_15_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_15_R2.fq.gz (100001 sequences in total) Input files are zr3644_15_R1.fq.gz_C_to_T.fastq and zr3644_15_R1.fq.gz_G_to_A.fastq and zr3644_15_R2.fq.gz_C_to_T.fastq and zr3644_15_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_15_R1.fq.gz_C_to_T.fastq and zr3644_15_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2157:1000_1:N:0:NCTCTACA+AGGAGGTA/1 99 NC_047568.1_CT_converted 1045333 0 24M1I90M = 1045396 192 ATAGAATAAAATATTATTTTATGGTTTTTTTAATTTTAAATATGAATTAAGGTATGTGTGTTTATAATATTTATGTGTTATTATTGTTTATTTTATTTGTTTTTATATTTTTATA FFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFF,F,FFFFFF:FFFFF:FFFF::FFFFFFFFFFF:FFFFFF AS:i:-38 XS:i:-32 XN:i:0 XM:i:5 XO:i:1 XG:i:1 NM:i:6 MD:Z:13G11G32T52T1G0 YS:i:-53 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2157:1000_2:N:0:NCTCTACA+AGGAGGTA/2 147 NC_047568.1_CT_converted 1045396 0 45M14D70M = 1045333 -192 TAATATTTATGTGTTATTATTGTTTATTTTATTTGTTTTTATATTTTTATATGGATTTTGGAATATTTTGAATTTTTTTTATTTAATTGATGTTTATTTATAGTTTTGTTTTTGA FFFF:FF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFF: AS:i:-53 XS:i:-59 XN:i:0 XM:i:1 XO:i:1 XG:i:14 NM:i:15 MD:Z:45^TTTTTGGAATATTA63A6 YS:i:-38 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_15_R1.fq.gz_G_to_A.fastq and zr3644_15_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2157:1000_1:N:0:NCTCTACA+AGGAGGTA/1 77 * 0 0 * * 0 0 ATAAAATAAAATATTATTTTATAATTTTTTTAATTTTAAATATAAATTAAAATATATATATTTATAATATTTATATATTATTATTATTTATTTTATTTATTTTTATATTTTTATA FFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFF,F,FFFFFF:FFFFF:FFFF::FFFFFFFFFFF:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2157:1000_2:N:0:NCTCTACA+AGGAGGTA/2 141 * 0 0 * * 0 0 TTAAAAATAAAATTATAAATAAATATTAATTAAATAAAAAAAATTTAAAATATTTTAAAATTTATATAAAAATATAAAAATAAATAAAATAAATAATAATAATATATAAATATTA :FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_15_R1.fq.gz_G_to_A.fastq and zr3644_15_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2157:1000_1:N:0:NCTCTACA+AGGAGGTA/1 77 * 0 0 * * 0 0 ATAAAATAAAATATTATTTTATAATTTTTTTAATTTTAAATATAAATTAAAATATATATATTTATAATATTTATATATTATTATTATTTATTTTATTTATTTTTATATTTTTATA FFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFF,F,FFFFFF:FFFFF:FFFF::FFFFFFFFFFF:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2157:1000_2:N:0:NCTCTACA+AGGAGGTA/2 141 * 0 0 * * 0 0 TTAAAAATAAAATTATAAATAAATATTAATTAAATAAAAAAAATTTAAAATATTTTAAAATTTATATAAAAATATAAAAATAAATAAAATAAATAATAATAATATATAAATATTA :FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_15_R1.fq.gz_C_to_T.fastq and zr3644_15_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2157:1000_1:N:0:NCTCTACA+AGGAGGTA/1 83 NC_047561.1_GA_converted 33259344 2 84M1I30M = 33259266 -192 TATAAAAATATAAAAACAAATAAAATAAACAATAATAACACATAAATATTATAAACACACATACCTTAATTCATATTTAAAATTAAAAAAACCATAAAATAATATTTTATTCTAT FFFFFF:FFFFFFFFFFF::FFFF:FFFFF:FFFFFF,F,FFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFF AS:i:-32 XS:i:-34 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:0C1A52A44C13 YS:i:-53 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2157:1000_2:N:0:NCTCTACA+AGGAGGTA/2 163 NC_047561.1_GA_converted 33259266 2 67M14D48M = 33259344 192 TCAAAAACAAAACTATAAATAAACATCAATTAAATAAAAAAAATTCAAAATATTCCAAAATCCATATAAAAATATAAAAACAAATAAAATAAACAATAATAACACATAAATATTA :FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF:FFFF AS:i:-53 XS:i:-53 XN:i:0 XM:i:1 XO:i:1 XG:i:14 NM:i:15 MD:Z:6T60^AAAAAATATTTCAA48 YS:i:-32 YT:Z:CP >>> Writing bisulfite mapping results to zr3644_15_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_15_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73244 (73.24%) aligned concordantly 0 times100000 reads; of these: 11898 (10000011.90 (%) aligned concordantly exactly 1 time 14858 (100.0014.86%%) were paired; of these:) aligned concordantly >1 times 26.7672976% ( overall alignment rate72.98 %) aligned concordantly 0 times 12181 (12.18%) aligned concordantly exactly 1 time 14843 (14.84%) aligned concordantly >1 times 27.02% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72936 (72.94%) aligned concordantly 0 times 12166 (12.17%) aligned concordantly exactly 1 time 14898 (14.90%) aligned concordantly >1 times 27.06% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73011 (73.01%) aligned concordantly 0 times 12123 (12.12%) aligned concordantly exactly 1 time 14866 (14.87%) aligned concordantly >1 times 26.99% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_15_R1.fq.gz_C_to_T.fastq, zr3644_15_R1.fq.gz_G_to_A.fastq, zr3644_15_R2.fq.gz_C_to_T.fastq and zr3644_15_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61418 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 21905 Sequence pairs did not map uniquely: 16677 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15110 ((converted) top strand) GA/CT/CT: 15436 (complementary to (converted) top strand) GA/CT/GA: 15403 (complementary to (converted) bottom strand) CT/GA/GA: 15469 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2166668 Total methylated C's in CpG context: 30900 Total methylated C's in CHG context: 1839 Total methylated C's in CHH context: 7454 Total methylated C's in Unknown context: 91 Total unmethylated C's in CpG context: 248157 Total unmethylated C's in CHG context: 374324 Total unmethylated C's in CHH context: 1503994 Total unmethylated C's in Unknown context: 5309 C methylated in CpG context: 11.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.7% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_16_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_16_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_16_R1.fq.gz Writing a C -> T converted version of the input file zr3644_16_R1.fq.gz to zr3644_16_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_16_R1.fq.gz to zr3644_16_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_16_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fq.gz Writing a C -> T converted version of the input file zr3644_16_R2.fq.gz to zr3644_16_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_16_R2.fq.gz to zr3644_16_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_16_R2.fq.gz (100001 sequences in total) Input files are zr3644_16_R1.fq.gz_C_to_T.fastq and zr3644_16_R1.fq.gz_G_to_A.fastq and zr3644_16_R2.fq.gz_C_to_T.fastq and zr3644_16_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_16_R1.fq.gz_C_to_T.fastq and zr3644_16_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1470:1000_1:N:0:NGAGCGTG+ACTTACGG/1 99 NC_047567.1_CT_converted 14590834 42 113M = 14590861 141 TAGAATTGTTTAATTTGTTTATTGTATTGTAAATTTTTGTGTTGAAAATTTGTGTATTGTTTATTGATGATGTTTTTTTATTTTTTAAGTTTTTTTAGTTTTGTTTTGTATTA FFFFFFFFFFFFFFFFFFF:FFFFFF:F,FFFF:FFFFFFFFFFFFF:FFFFFF:F:FFFFFFFFFFFF,F,FFFFF,FFFFFFFFFFFFFF,:FFF:::,FFFFFF,FFFFF AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:77G14G16G3 YS:i:-6 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1470:1000_2:N:0:NGAGCGTG+ACTTACGG/2 147 NC_047567.1_CT_converted 14590861 42 114M = 14590834 -141 TGTAAATTTTTGTGTTGAAAATTTGTGTATTGTTTATTGATGATGTTTTTGTATTTTTTAAGTTTGTTTAGTTTTGTTTTGTATTAAGTTGGTAGTGGGTATAGTGGGTTGTGA FFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF,FFFFFF::FFFFF:FFFFFF,FFF:,FFF,FFFF,FFFFFFF::FF:FFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:82G31 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_16_R1.fq.gz_G_to_A.fastq and zr3644_16_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1470:1000_1:N:0:NGAGCGTG+ACTTACGG/1 77 * 0 0 * * 0 0 TAAAATTATTTAATTTATTTATTATATTATAAATTTTTATATTAAAAATTTATATATTATTTATTAATAATATTTTTTTATTTTTTAAATTTTTTTAATTTTATTTTATATTA FFFFFFFFFFFFFFFFFFF:FFFFFF:F,FFFF:FFFFFFFFFFFFF:FFFFFF:F:FFFFFFFFFFFF,F,FFFFF,FFFFFFFFFFFFFF,:FFF:::,FFFFFF,FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1470:1000_2:N:0:NGAGCGTG+ACTTACGG/2 141 * 0 0 * * 0 0 TTATAATTTATTATATTTATTATTAATTTAATATAAAATAAAATTAAATAAATTTAAAAAATATAAAAATATTATTAATAAATAATATATAAATTTTTAATATAAAAATTTATA FFFFFFFFFFFFFFFF:FF::FFFFFFF,FFFF,FFF,:FFF,FFFFFF:FFFFF::FFFFFF,FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_16_R1.fq.gz_G_to_A.fastq and zr3644_16_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1470:1000_1:N:0:NGAGCGTG+ACTTACGG/1 77 * 0 0 * * 0 0 TAAAATTATTTAATTTATTTATTATATTATAAATTTTTATATTAAAAATTTATATATTATTTATTAATAATATTTTTTTATTTTTTAAATTTTTTTAATTTTATTTTATATTA FFFFFFFFFFFFFFFFFFF:FFFFFF:F,FFFF:FFFFFFFFFFFFF:FFFFFF:F:FFFFFFFFFFFF,F,FFFFF,FFFFFFFFFFFFFF,:FFF:::,FFFFFF,FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1470:1000_2:N:0:NGAGCGTG+ACTTACGG/2 141 * 0 0 * * 0 0 TTATAATTTATTATATTTATTATTAATTTAATATAAAATAAAATTAAATAAATTTAAAAAATATAAAAATATTATTAATAAATAATATATAAATTTTTAATATAAAAATTTATA FFFFFFFFFFFFFFFF:FF::FFFFFFF,FFFF,FFF,:FFF,FFFFFF:FFFFF::FFFFFF,FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_16_R1.fq.gz_C_to_T.fastq and zr3644_16_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1470:1000_1:N:0:NGAGCGTG+ACTTACGG/1 83 NC_047561.1_GA_converted 13314203 23 113M = 13314175 -141 TAATACAAAACAAAACTAAAAAAACTTAAAAAATAAAAAAACATCATCAATAAACAATACACAAATTTTCAACACAAAAATTTACAATACAATAAACAAATTAAACAATTCTA FFFFF,FFFFFF,:::FFF:,FFFFFFFFFFFFFF,FFFFF,F,FFFFFFFFFFFF:F:FFFFFF:FFFFFFFFFFFFF:FFFF,F:FFFFFF:FFFFFFFFFFFFFFFFFFF AS:i:-42 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:3C16C14C31A2T16C17A7 YS:i:-24 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1470:1000_2:N:0:NGAGCGTG+ACTTACGG/2 163 NC_047561.1_GA_converted 13314175 23 114M = 13314203 141 TCACAACCCACTATACCCACTACCAACTTAATACAAAACAAAACTAAACAAACTTAAAAAATACAAAAACATCATCAATAAACAATACACAAATTTTCAACACAAAAATTTACA FFFFFFFFFFFFFFFF:FF::FFFFFFF,FFFF,FFF,:FFF,FFFFFF:FFFFF::FFFFFF,FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFF AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:13A17C63A2T15 YS:i:-42 YT:Z:CP >>> Writing bisulfite mapping results to zr3644_16_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_16_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72582 (72.58%) aligned concordantly 0 times 12330 (12.33%) aligned concordantly exactly 1 time 15088 (15.09%) aligned concordantly >1 times 27.42% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 100000 reads; of these:72878 ( 72.88100000% () aligned concordantly 0 times 11931 (100.0011.93%%) were paired; of these:) aligned concordantly exactly 1 time 7192715191 ( (71.9315.19%%) aligned concordantly 0 times) aligned concordantly >1 times 27.1212347% ( overall alignment rate12.35 %) aligned concordantly exactly 1 time 15726 (15.73%) aligned concordantly >1 times 28.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71943 (71.94%) aligned concordantly 0 times 12366 (12.37%) aligned concordantly exactly 1 time 15691 (15.69%) aligned concordantly >1 times 28.06% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_16_R1.fq.gz_C_to_T.fastq, zr3644_16_R1.fq.gz_G_to_A.fastq, zr3644_16_R2.fq.gz_C_to_T.fastq and zr3644_16_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61736 Mapping efficiency: 61.7% Sequence pairs with no alignments under any condition: 20553 Sequence pairs did not map uniquely: 17711 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15421 ((converted) top strand) GA/CT/CT: 15520 (complementary to (converted) top strand) GA/CT/GA: 15692 (complementary to (converted) bottom strand) CT/GA/GA: 15103 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2142951 Total methylated C's in CpG context: 29209 Total methylated C's in CHG context: 1885 Total methylated C's in CHH context: 7823 Total methylated C's in Unknown context: 69 Total unmethylated C's in CpG context: 250460 Total unmethylated C's in CHG context: 373429 Total unmethylated C's in CHH context: 1480145 Total unmethylated C's in Unknown context: 5147 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_17_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_17_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_17_R1.fq.gz Writing a C -> T converted version of the input file zr3644_17_R1.fq.gz to zr3644_17_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_17_R1.fq.gz to zr3644_17_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_17_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fq.gz Writing a C -> T converted version of the input file zr3644_17_R2.fq.gz to zr3644_17_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_17_R2.fq.gz to zr3644_17_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_17_R2.fq.gz (100001 sequences in total) Input files are zr3644_17_R1.fq.gz_C_to_T.fastq and zr3644_17_R1.fq.gz_G_to_A.fastq and zr3644_17_R2.fq.gz_C_to_T.fastq and zr3644_17_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_17_R1.fq.gz_C_to_T.fastq and zr3644_17_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1759:1000_1:N:0:NAAGCATC+AATGGATT/1 77 * 0 0 * * 0 0 AAATTAAATATTATAATTAAATATTATTATATTAATTTTTATATTTATTATTTAATTAATTTATTAAATTTATAAAATTATATATTTATAATTTATATTATTAAAAAAATATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFF:FF:FFFF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1759:1000_2:N:0:NAAGCATC+AATGGATT/2 141 * 0 0 * * 0 0 TATATTTTATTAAATATTTTTTTAATAATATAAATTATAAATATATAATTTTATAAATTTAATAAATTAATTAAATAATAAATATAAAAATTAATATAATAATATTTAATTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_17_R1.fq.gz_G_to_A.fastq and zr3644_17_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1759:1000_1:N:0:NAAGCATC+AATGGATT/1 77 * 0 0 * * 0 0 AAATTAAACATCACAATTAAACACCATTACATTAATTTCTACATCCATTATTTAATCAACCTATCAAATTCACAAAATTATATATTTATAATCTACACTACTAAAAAAATACCCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFF:FF:FFFF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1759:1000_2:N:0:NAAGCATC+AATGGATT/2 141 * 0 0 * * 0 0 TATATTTTGTTGGGTATTTTTTTAGTAGTGTAGATTATAAATATATAATTTTGTGAATTTGATAGGTTGATTAAATAATGGATGTAGAAATTAATGTAATGGTGTTTAATTGTGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_17_R1.fq.gz_G_to_A.fastq and zr3644_17_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1759:1000_1:N:0:NAAGCATC+AATGGATT/1 77 * 0 0 * * 0 0 AAATTAAACATCACAATTAAACACCATTACATTAATTTCTACATCCATTATTTAATCAACCTATCAAATTCACAAAATTATATATTTATAATCTACACTACTAAAAAAATACCCA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFF:FF:FFFF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1759:1000_2:N:0:NAAGCATC+AATGGATT/2 141 * 0 0 * * 0 0 TATATTTTGTTGGGTATTTTTTTAGTAGTGTAGATTATAAATATATAATTTTGTGAATTTGATAGGTTGATTAAATAATGGATGTAGAAATTAATGTAATGGTGTTTAATTGTGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_17_R1.fq.gz_C_to_T.fastq and zr3644_17_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1759:1000_1:N:0:NAAGCATC+AATGGATT/1 77 * 0 0 * * 0 0 AAATTAAATATTATAATTAAATATTATTATATTAATTTTTATATTTATTATTTAATTAATTTATTAAATTTATAAAATTATATATTTATAATTTATATTATTAAAAAAATATTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFF:FF:FFFF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1759:1000_2:N:0:NAAGCATC+AATGGATT/2 141 * 0 0 * * 0 0 TATATTTTATTAAATATTTTTTTAATAATATAAATTATAAATATATAATTTTATAAATTTAATAAATTAATTAAATAATAAATATAAAAATTAATATAATAATATTTAATTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_17_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_17_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72405 (72.41%) aligned concordantly 0 times 12348 (12.35%) aligned concordantly exactly 1 time 15247 (15.25%) aligned concordantly >1 times 27.59% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72357 (72.36%) aligned concordantly 0 times 12271 (12.27%) aligned concordantly exactly 1 time 15372 (15.37%) aligned concordantly >1 times 27.64% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72285 (72.28%) aligned concordantly 0 times 12433 (12.43%) aligned concordantly exactly 1 time 15282 (15.28%) aligned concordantly >1 times 27.71% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72529 (72.53%) aligned concordantly 0 times 12224 (12.22%) aligned concordantly exactly 1 time 15247 (15.25%) aligned concordantly >1 times 27.47% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_17_R1.fq.gz_C_to_T.fastq, zr3644_17_R1.fq.gz_G_to_A.fastq, zr3644_17_R2.fq.gz_C_to_T.fastq and zr3644_17_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61805 Mapping efficiency: 61.8% Sequence pairs with no alignments under any condition: 20526 Sequence pairs did not map uniquely: 17669 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15182 ((converted) top strand) GA/CT/CT: 15650 (complementary to (converted) top strand) GA/CT/GA: 15428 (complementary to (converted) bottom strand) CT/GA/GA: 15545 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2184728 Total methylated C's in CpG context: 29618 Total methylated C's in CHG context: 1881 Total methylated C's in CHH context: 7761 Total methylated C's in Unknown context: 75 Total unmethylated C's in CpG context: 260260 Total unmethylated C's in CHG context: 382957 Total unmethylated C's in CHH context: 1502251 Total unmethylated C's in Unknown context: 5205 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_18_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_18_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_18_R1.fq.gz Writing a C -> T converted version of the input file zr3644_18_R1.fq.gz to zr3644_18_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_18_R1.fq.gz to zr3644_18_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_18_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fq.gz Writing a C -> T converted version of the input file zr3644_18_R2.fq.gz to zr3644_18_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_18_R2.fq.gz to zr3644_18_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_18_R2.fq.gz (100001 sequences in total) Input files are zr3644_18_R1.fq.gz_C_to_T.fastq and zr3644_18_R1.fq.gz_G_to_A.fastq and zr3644_18_R2.fq.gz_C_to_T.fastq and zr3644_18_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_18_R1.fq.gz_C_to_T.fastq and zr3644_18_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1741:1000_1:N:0:NCTTCAAG+TTCATGGT/1 77 * 0 0 * * 0 0 TAATAATAATAATTTTTATATTTTATTAAATTATTTATATTAATTAAATTAATTAATTATTATTATATATAATTTTATAATTAAAATATTAAATTTATAAATTATAAATTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1741:1000_2:N:0:NCTTCAAG+TTCATGGT/2 141 * 0 0 * * 0 0 ATATATAAATTAAAATAAAAAATTATAATTTTAAAAAATTTAATAAATATAAAAAAAATTTTAAATAAATTTAAATTTATAATTTATAATTTATAAATTTAATATTTTAATTATA :FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF:FFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_18_R1.fq.gz_G_to_A.fastq and zr3644_18_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1741:1000_1:N:0:NCTTCAAG+TTCATGGT/1 77 * 0 0 * * 0 0 TAACAATAACAATTTTCATATTTTATTAAACTATTTATATCAATCAAACTAATTAACTATCATCATATATAACTCTATAATTAAAATATCAAACTTATAAACCACAAATTACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1741:1000_2:N:0:NCTTCAAG+TTCATGGT/2 141 * 0 0 * * 0 0 ATATGTAAATTAGGATGAAAAATTATGATTTTAAAAAATTTAATAAATATGAAAAAAGTTTTAGATGGATTTGAATTTGTAATTTGTGGTTTATAAGTTTGATATTTTAATTATA :FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF:FFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_18_R1.fq.gz_G_to_A.fastq and zr3644_18_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1741:1000_1:N:0:NCTTCAAG+TTCATGGT/1 77 * 0 0 * * 0 0 TAACAATAACAATTTTCATATTTTATTAAACTATTTATATCAATCAAACTAATTAACTATCATCATATATAACTCTATAATTAAAATATCAAACTTATAAACCACAAATTACAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1741:1000_2:N:0:NCTTCAAG+TTCATGGT/2 141 * 0 0 * * 0 0 ATATGTAAATTAGGATGAAAAATTATGATTTTAAAAAATTTAATAAATATGAAAAAAGTTTTAGATGGATTTGAATTTGTAATTTGTGGTTTATAAGTTTGATATTTTAATTATA :FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF:FFFFFFFFFFFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_18_R1.fq.gz_C_to_T.fastq and zr3644_18_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1741:1000_1:N:0:NCTTCAAG+TTCATGGT/1 77 * 0 0 * * 0 0 TAATAATAATAATTTTTATATTTTATTAAATTATTTATATTAATTAAATTAATTAATTATTATTATATATAATTTTATAATTAAAATATTAAATTTATAAATTATAAATTATAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1741:1000_2:N:0:NCTTCAAG+TTCATGGT/2 141 * 0 0 * * 0 0 ATATATAAATTAAAATAAAAAATTATAATTTTAAAAAATTTAATAAATATAAAAAAAATTTTAAATAAATTTAAATTTATAATTTATAATTTATAAATTTAATATTTTAATTATA :FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF:FFFFFFFFFFFF:FFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_18_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_18_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72778 (72.78%) aligned concordantly 0 times 12533 (12.53%) aligned concordantly exactly 1 time 14689 (14.69%) aligned concordantly >1 times 27.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72944 (72.94%) aligned concordantly 0 times 12327 (12.33%) aligned concordantly exactly 1 time 14729 (14.73%) aligned concordantly >1 times 27.06% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72445 (72.44%) aligned concordantly 0 times 12487 (12.49%) aligned concordantly exactly 1 time 15068 (15.07%) aligned concordantly >1 times 27.55% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72606 (72.61%) aligned concordantly 0 times 12446 (12.45%) aligned concordantly exactly 1 time 14948 (14.95%) aligned concordantly >1 times 27.39% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_18_R1.fq.gz_C_to_T.fastq, zr3644_18_R1.fq.gz_G_to_A.fastq, zr3644_18_R2.fq.gz_C_to_T.fastq and zr3644_18_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 62397 Mapping efficiency: 62.4% Sequence pairs with no alignments under any condition: 20763 Sequence pairs did not map uniquely: 16840 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15525 ((converted) top strand) GA/CT/CT: 15680 (complementary to (converted) top strand) GA/CT/GA: 15544 (complementary to (converted) bottom strand) CT/GA/GA: 15648 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2194162 Total methylated C's in CpG context: 29865 Total methylated C's in CHG context: 1793 Total methylated C's in CHH context: 7718 Total methylated C's in Unknown context: 60 Total unmethylated C's in CpG context: 257540 Total unmethylated C's in CHG context: 384284 Total unmethylated C's in CHH context: 1512962 Total unmethylated C's in Unknown context: 5240 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_19_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_19_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_19_R1.fq.gz Writing a C -> T converted version of the input file zr3644_19_R1.fq.gz to zr3644_19_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_19_R1.fq.gz to zr3644_19_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_19_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fq.gz Writing a C -> T converted version of the input file zr3644_19_R2.fq.gz to zr3644_19_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_19_R2.fq.gz to zr3644_19_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_19_R2.fq.gz (100001 sequences in total) Input files are zr3644_19_R1.fq.gz_C_to_T.fastq and zr3644_19_R1.fq.gz_G_to_A.fastq and zr3644_19_R2.fq.gz_C_to_T.fastq and zr3644_19_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_19_R1.fq.gz_C_to_T.fastq and zr3644_19_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1615:1000_1:N:0:NCAGAAGG+TATGATGG/1 77 * 0 0 * * 0 0 TGTTTATTTTTTATAATTATTATTAAAAAAAATAATAATAATTTTGAATTTTTTTAAAATTTATATATATATAATTATATTAAATATTTATAAATAATTTTAAAATATTTTTAAA FFFFFFFFFFFF::FF:,:FF::FFF:FFFFFFFFF:FFFFFFFFFFFF:F:FFFFFF:FFF:FF,F:FFF:,FFFFFFFFFF:FFFFFF,FFFF:F:FFF::FFFFFFFFFFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1615:1000_2:N:0:NCAGAAGG+TATGATGG/2 141 * 0 0 * * 0 0 TTTAAAAATATTTTAAAATTATTTATAAATATTTAATATAATTATATATATATAAATTTTAAAAAAATTCAAAATTATTATTATTTTTTTTAATAATAATTATAAAAAATAAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_19_R1.fq.gz_G_to_A.fastq and zr3644_19_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1615:1000_1:N:0:NCAGAAGG+TATGATGG/1 99 NC_047568.1_GA_converted 39689236 42 115M = 39689236 -115 CATTCATTTTCTACAACCACTATCAAAAAAAATAATAATAACCTCAAATTTCTTCAAAATTCATACATACATAATTATATCAAATATTTACAAATAACTTTAAAACACTTTTAAA FFFFFFFFFFFF::FF:,:FF::FFF:FFFFFFFFF:FFFFFFFFFFFF:F:FFFFFF:FFF:FF,F:FFF:,FFFFFFFFFF:FFFFFF,FFFF:F:FFF::FFFFFFFFFFF: AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:41T73 YS:i:-6 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1615:1000_2:N:0:NCAGAAGG+TATGATGG/2 147 NC_047568.1_GA_converted 39689236 42 115M = 39689236 -115 CATTCATTTTCTACAACCACTATCAAAAAAAATAATAATAACCTCAAATTTCTTCAAAATTCATACATACATAATTATATCAAATATTTACAAATAACTTTAAAACACTTTTAAA FFFFFF:FFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF:FF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:41T73 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_19_R1.fq.gz_G_to_A.fastq and zr3644_19_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1615:1000_1:N:0:NCAGAAGG+TATGATGG/1 77 * 0 0 * * 0 0 CATTCATTTTCTACAACCACTATCAAAAAAAATAATAATAACCTCAAATTTCTTCAAAATTCATACATACATAATTATATCAAATATTTACAAATAACTTTAAAACACTTTTAAA FFFFFFFFFFFF::FF:,:FF::FFF:FFFFFFFFF:FFFFFFFFFFFF:F:FFFFFF:FFF:FF,F:FFF:,FFFFFFFFFF:FFFFFF,FFFF:F:FFF::FFFFFFFFFFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1615:1000_2:N:0:NCAGAAGG+TATGATGG/2 141 * 0 0 * * 0 0 TTTAAAAGTGTTTTAAAGTTATTTGTAAATATTTGATATAATTATGTATGTATGAATTTTGAAGAAATTTGAGGTTATTATTATTTTTTTTGATAGTGGTTGTAGAAAATGAATG FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_19_R1.fq.gz_C_to_T.fastq and zr3644_19_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1615:1000_1:N:0:NCAGAAGG+TATGATGG/1 77 * 0 0 * * 0 0 TGTTTATTTTTTATAATTATTATTAAAAAAAATAATAATAATTTTGAATTTTTTTAAAATTTATATATATATAATTATATTAAATATTTATAAATAATTTTAAAATATTTTTAAA FFFFFFFFFFFF::FF:,:FF::FFF:FFFFFFFFF:FFFFFFFFFFFF:F:FFFFFF:FFF:FF,F:FFF:,FFFFFFFFFF:FFFFFF,FFFF:F:FFF::FFFFFFFFFFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1615:1000_2:N:0:NCAGAAGG+TATGATGG/2 141 * 0 0 * * 0 0 TTTAAAAATATTTTAAAATTATTTATAAATATTTAATATAATTATATATATATAAATTTTAAAAAAATTCAAAATTATTATTATTTTTTTTAATAATAATTATAAAAAATAAACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFF:FFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_19_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_19_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72968 (72.97%) aligned concordantly 0 times 11753 (11.75%) aligned concordantly exactly 1 time 15279 (15.28%) aligned concordantly >1 times 27.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72795 (72.80%) aligned concordantly 0 times 12155 (12.15%) aligned concordantly exactly 1 time 15050 (15.05%) aligned concordantly >1 times 27.20% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72843 (72.84%) aligned concordantly 0 times 12253 (12.25%) aligned concordantly exactly 1 time 14904 (14.90%) aligned concordantly >1 times 27.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72608 (72.61%) aligned concordantly 0 times 12050 (12.05%) aligned concordantly exactly 1 time 15342 (15.34%) aligned concordantly >1 times 27.39% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_19_R1.fq.gz_C_to_T.fastq, zr3644_19_R1.fq.gz_G_to_A.fastq, zr3644_19_R2.fq.gz_C_to_T.fastq and zr3644_19_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61402 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 21445 Sequence pairs did not map uniquely: 17153 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15058 ((converted) top strand) GA/CT/CT: 15440 (complementary to (converted) top strand) GA/CT/GA: 15449 (complementary to (converted) bottom strand) CT/GA/GA: 15455 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2151706 Total methylated C's in CpG context: 27843 Total methylated C's in CHG context: 1773 Total methylated C's in CHH context: 7762 Total methylated C's in Unknown context: 53 Total unmethylated C's in CpG context: 250344 Total unmethylated C's in CHG context: 372609 Total unmethylated C's in CHH context: 1491375 Total unmethylated C's in Unknown context: 5466 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.0% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_1_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_1_R1.fq.gz Writing a C -> T converted version of the input file zr3644_1_R1.fq.gz to zr3644_1_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_1_R1.fq.gz to zr3644_1_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_1_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fq.gz Writing a C -> T converted version of the input file zr3644_1_R2.fq.gz to zr3644_1_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_1_R2.fq.gz to zr3644_1_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_1_R2.fq.gz (100001 sequences in total) Input files are zr3644_1_R1.fq.gz_C_to_T.fastq and zr3644_1_R1.fq.gz_G_to_A.fastq and zr3644_1_R2.fq.gz_C_to_T.fastq and zr3644_1_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_1_R1.fq.gz_C_to_T.fastq and zr3644_1_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2049:1000_1:N:0:NGTTGCGA+TTGCTCTA/1 77 * 0 0 * * 0 0 TAAATTTTTATTAATAATAATAATAATATTTTAATAAATAAAAAAATATTTATATATATTTTTTAAAATTTTATATAAAATAAATATTAATTAAAATAAATTTATTTTTTATATA FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2049:1000_2:N:0:NGTTGCGA+TTGCTCTA/2 141 * 0 0 * * 0 0 TATAATATATAAAAAATAAATTTATTTTAATTAATATTTATTTTATATAAAATTTTAAAAAATATATATAAATATTTTTTTATTTATTAAAATATTATTATTATTATTAATAAAA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFF:FFFFF:F:FFFF:FFF:FFFFFFF,:FFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_1_R1.fq.gz_G_to_A.fastq and zr3644_1_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2049:1000_1:N:0:NGTTGCGA+TTGCTCTA/1 99 NC_047560.1_GA_converted 10931927 23 115M = 10931932 120 TAAATTTTTACCAATAACAACAACAACATCTCAACAAATAAAAAAACATTCACACATATCTTTTAAAATCTCATATAAAACAAACACTAATTAAAACAAACTTACCCCCTATACA FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:12T42C0A19C27A10 YS:i:-30 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2049:1000_2:N:0:NGTTGCGA+TTGCTCTA/2 147 NC_047560.1_GA_converted 10931932 23 115M = 10931927 -120 TTTTACCAATAACAACAACAACATCTCAACAAATAAAAAAACATTCACACATATCTTTTAAAATCTCATATAAAACAAACACTAATTAAAACAAACTTACCCCCTATACATTATA FFFFFFF:,FFFFFFF:FFF:FFFF:F:FFFFF:FFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:7T42C0A19C27A15 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_1_R1.fq.gz_G_to_A.fastq and zr3644_1_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2049:1000_1:N:0:NGTTGCGA+TTGCTCTA/1 83 NC_047560.1_CT_converted 2448360 23 115M = 2448355 -120 TGTATAGGGGGTAAGTTTGTTTTAATTAGTGTTTGTTTTATATGAGATTTTAAAAGATATGTGTGAATGTTTTTTTATTTGTTGAGATGTTGTTGTTGTTATTGGTAAAAATTTA FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:10T27G19T0G42A12 YS:i:-30 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2049:1000_2:N:0:NGTTGCGA+TTGCTCTA/2 163 NC_047560.1_CT_converted 2448355 23 115M = 2448360 120 TATAATGTATAGGGGGTAAGTTTGTTTTAATTAGTGTTTGTTTTATATGAGATTTTAAAAGATATGTGTGAATGTTTTTTTATTTGTTGAGATGTTGTTGTTGTTATTGGTAAAA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFF:FFFFF:F:FFFF:FFF:FFFFFFF,:FFFFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:15T27G19T0G42A7 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_1_R1.fq.gz_C_to_T.fastq and zr3644_1_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2049:1000_1:N:0:NGTTGCGA+TTGCTCTA/1 77 * 0 0 * * 0 0 TAAATTTTTATTAATAATAATAATAATATTTTAATAAATAAAAAAATATTTATATATATTTTTTAAAATTTTATATAAAATAAATATTAATTAAAATAAATTTATTTTTTATATA FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2049:1000_2:N:0:NGTTGCGA+TTGCTCTA/2 141 * 0 0 * * 0 0 TATAATATATAAAAAATAAATTTATTTTAATTAATATTTATTTTATATAAAATTTTAAAAAATATATATAAATATTTTTTTATTTATTAAAATATTATTATTATTATTAATAAAA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFF:FFFFF:F:FFFF:FFF:FFFFFFF,:FFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72231 (72.23%) aligned concordantly 0 times 12547 (12.55%) aligned concordantly exactly 1 time 15222 (15.22%) aligned concordantly >1 times 27.77% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72404 (72.40%) aligned concordantly 0 times 12234 (12.23%) aligned concordantly exactly 1 time 15362 (15.36%) aligned concordantly >1 times 27.60% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72515 (72.52%) aligned concordantly 0 times 12357 (12.36%) aligned concordantly exactly 1 time 15128 (15.13%) aligned concordantly >1 times 27.48% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72498 (72.50%) aligned concordantly 0 times 12348 (12.35%) aligned concordantly exactly 1 time 15154 (15.15%) aligned concordantly >1 times 27.50% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_1_R1.fq.gz_C_to_T.fastq, zr3644_1_R1.fq.gz_G_to_A.fastq, zr3644_1_R2.fq.gz_C_to_T.fastq and zr3644_1_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 62534 Mapping efficiency: 62.5% Sequence pairs with no alignments under any condition: 20244 Sequence pairs did not map uniquely: 17222 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15602 ((converted) top strand) GA/CT/CT: 15606 (complementary to (converted) top strand) GA/CT/GA: 15523 (complementary to (converted) bottom strand) CT/GA/GA: 15803 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2197155 Total methylated C's in CpG context: 26938 Total methylated C's in CHG context: 1753 Total methylated C's in CHH context: 7196 Total methylated C's in Unknown context: 58 Total unmethylated C's in CpG context: 258523 Total unmethylated C's in CHG context: 384627 Total unmethylated C's in CHH context: 1518118 Total unmethylated C's in Unknown context: 5416 C methylated in CpG context: 9.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_20_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_20_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_20_R1.fq.gz Writing a C -> T converted version of the input file zr3644_20_R1.fq.gz to zr3644_20_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_20_R1.fq.gz to zr3644_20_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_20_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fq.gz Writing a C -> T converted version of the input file zr3644_20_R2.fq.gz to zr3644_20_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_20_R2.fq.gz to zr3644_20_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_20_R2.fq.gz (100001 sequences in total) Input files are zr3644_20_R1.fq.gz_C_to_T.fastq and zr3644_20_R1.fq.gz_G_to_A.fastq and zr3644_20_R2.fq.gz_C_to_T.fastq and zr3644_20_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_20_R1.fq.gz_C_to_T.fastq and zr3644_20_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2790:1000_1:N:0:NCGTTGGT+GGAAGTAT/1 99 NC_047566.1_CT_converted 30638354 23 42M1D73M = 30638504 265 AAATAATGTTGGTATATATTAATTTGTATTTTTTTTTAATTATTTATAATTTAATTTAAATTATATGAGTGTTTTTTAAATTAGTAAAGTGATTGTATTTGTGTTTAAGGTGATT FFFFFFFF,FF,F:F:FFF:F::FFFF:F,F:FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF,FF:FFF:FFF,FF:FF:,FFFF:FFFFF AS:i:-32 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:27T14^T22T6G37A5 YS:i:-30 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2790:1000_2:N:0:NCGTTGGT+GGAAGTAT/2 147 NC_047566.1_CT_converted 30638504 23 115M = 30638354 -265 GGTATGTTTTTAATGATAGAATGTGTATAAAGAGAGGTTATTTTTTTTAATAGAAGTTTTTGTTTTTGAGTTGATGGAATAAATTTTAGATTGTTAAGTTTTGTTTTATTTTTTA ::FFFF:FFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:29T3A46G22G10G0 YS:i:-32 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_20_R1.fq.gz_G_to_A.fastq and zr3644_20_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2790:1000_1:N:0:NCGTTGGT+GGAAGTAT/1 77 * 0 0 * * 0 0 AAATAATATTAATATATATTAATTTATATTTTTTTTTAATTATTTATAATTTAATTTAAATTATATAAATATTCTTTAAATTAATAAAATAATTATATTTATATTTAAAATAATT FFFFFFFF,FF,F:F:FFF:F::FFFF:F,F:FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF,FF:FFF:FFF,FF:FF:,FFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2790:1000_2:N:0:NCGTTGGT+GGAAGTAT/2 141 * 0 0 * * 0 0 TAAAAAATAAAATAAAATTTAATAATTTAAAATTTATTTTATTAATTTAAAAATAAAAATTTTTATTAAAAAAAATAATTTTTTTTTATATATATTTTATTATTAAAAATATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFFF:: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_20_R1.fq.gz_G_to_A.fastq and zr3644_20_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2790:1000_1:N:0:NCGTTGGT+GGAAGTAT/1 77 * 0 0 * * 0 0 AAATAATATTAATATATATTAATTTATATTTTTTTTTAATTATTTATAATTTAATTTAAATTATATAAATATTCTTTAAATTAATAAAATAATTATATTTATATTTAAAATAATT FFFFFFFF,FF,F:F:FFF:F::FFFF:F,F:FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF,FF:FFF:FFF,FF:FF:,FFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2790:1000_2:N:0:NCGTTGGT+GGAAGTAT/2 141 * 0 0 * * 0 0 TAAAAAATAAAATAAAATTTAATAATTTAAAATTTATTTTATTAATTTAAAAATAAAAATTTTTATTAAAAAAAATAATTTTTTTTTATATATATTTTATTATTAAAAATATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFFF:: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_20_R1.fq.gz_C_to_T.fastq and zr3644_20_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2790:1000_1:N:0:NCGTTGGT+GGAAGTAT/1 77 * 0 0 * * 0 0 AAATAATGTTGGTATATATTAATTTGTATTTTTTTTTAATTATTTATAATTTAATTTAAATTATATGAGTGTTTTTTAAATTAGTAAAGTGATTGTATTTGTGTTTAAGGTGATT FFFFFFFF,FF,F:F:FFF:F::FFFF:F,F:FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF,FF:FFF:FFF,FF:FF:,FFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2790:1000_2:N:0:NCGTTGGT+GGAAGTAT/2 141 * 0 0 * * 0 0 TAAAAAATAAAACAAAACTTAACAATCTAAAATTTATTCCATCAACTCAAAAACAAAAACTTCTATTAAAAAAAATAACCTCTCTTTATACACATTCTATCATTAAAAACATACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFFF:: YT:Z:UP >>> Writing bisulfite mapping results to zr3644_20_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_20_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:9046:5228_1:N:0:GCGTTGGT+GGAAGTAT NC_001276.1 18111 Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:22516:19664_1:N:0:GCGTTGGT+GGAAGTAT NW_022994957.1 201032 100000 reads; of these: 100000 (100.00%) were paired; of these: 72350 (72.35%) aligned concordantly 0 times 12515 (12.52%) aligned concordantly exactly 1 time 15135 (15.13%) aligned concordantly >1 times 27.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73973 (73.97%) aligned concordantly 0 times 11894 (11.89%) aligned concordantly exactly 1 time 14133 (14.13%) aligned concordantly >1 times 26.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72362 (72.36%) aligned concordantly 0 times 12560 (12.56%) aligned concordantly exactly 1 time 15078 (15.08%) aligned concordantly >1 times 27.64% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73994 (73.99%) aligned concordantly 0 times 11840 (11.84%) aligned concordantly exactly 1 time 14166 (14.17%) aligned concordantly >1 times 26.01% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_20_R1.fq.gz_C_to_T.fastq, zr3644_20_R1.fq.gz_G_to_A.fastq, zr3644_20_R2.fq.gz_C_to_T.fastq and zr3644_20_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61594 Mapping efficiency: 61.6% Sequence pairs with no alignments under any condition: 21962 Sequence pairs did not map uniquely: 16444 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15039 ((converted) top strand) GA/CT/CT: 15791 (complementary to (converted) top strand) GA/CT/GA: 15787 (complementary to (converted) bottom strand) CT/GA/GA: 14975 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2172583 Total methylated C's in CpG context: 28191 Total methylated C's in CHG context: 1786 Total methylated C's in CHH context: 8067 Total methylated C's in Unknown context: 91 Total unmethylated C's in CpG context: 252733 Total unmethylated C's in CHG context: 376351 Total unmethylated C's in CHH context: 1505455 Total unmethylated C's in Unknown context: 5247 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.7% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_21_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_21_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_21_R1.fq.gz Writing a C -> T converted version of the input file zr3644_21_R1.fq.gz to zr3644_21_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_21_R1.fq.gz to zr3644_21_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_21_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fq.gz Writing a C -> T converted version of the input file zr3644_21_R2.fq.gz to zr3644_21_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_21_R2.fq.gz to zr3644_21_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_21_R2.fq.gz (100001 sequences in total) Input files are zr3644_21_R1.fq.gz_C_to_T.fastq and zr3644_21_R1.fq.gz_G_to_A.fastq and zr3644_21_R2.fq.gz_C_to_T.fastq and zr3644_21_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_21_R1.fq.gz_C_to_T.fastq and zr3644_21_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1723:1000_1:N:0:NCATATCC+ATTGCACA/1 77 * 0 0 * * 0 0 ATTTTTATATTAAAATAAATATATATTATTTTTTATAAAAAAATTTTTTAAATTTTATAAAATTTATAAATATTAAATAAAATTATTTTTATTAATTTTAAATAAATTATATATA FFF:::FFFFFFFF:FFF:FFFFF:FFFF,:FF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:,FFF,,FFFFFFF,,FFFF:FFF:FFF:F:FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1723:1000_2:N:0:NCATATCC+ATTGCACA/2 141 * 0 0 * * 0 0 AAAAAATAAATAATTATATATATAATTTATTTAAAATTAATAAAAATAATTTTATTTAATATTTATAAATTTTATAAAATTTAAAAAATTTTTTTATAAAAAATAATATATATTT FFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,::,FFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFF:F:FFFFF,:FF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_21_R1.fq.gz_G_to_A.fastq and zr3644_21_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1723:1000_1:N:0:NCATATCC+ATTGCACA/1 99 NC_047565.1_GA_converted 34399192 12 115M = 34399208 131 ATTCCCACACTAAAACAAATATACACCATCCTTCATAAAAAAATTTTTCAAATTCCATAAAATTTATAAATATTAAATAAAACTATCCCCATTAACCTTAAATAAATTACACATA FFF:::FFFFFFFF:FFF:FFFFF:FFFF,:FF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:,FFF,,FFFFFFF,,FFFF:FFF:FFF:F:FFF AS:i:-12 XS:i:-20 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7A4T102 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1723:1000_2:N:0:NCATATCC+ATTGCACA/2 147 NC_047565.1_GA_converted 34399208 12 115M = 34399192 -131 AAATATACACCATCCTTCATAAAAAAATTTTTCAAATTCCATAAAATTTATAAATATTAAATAAAACTATCCCCATTAACCTTAAATAAATTACACATATAATTATTTATTCTTT FFFFFFFFFF:FF:,FFFFF:F:FFFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFF,::,FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFF AS:i:0 XS:i:-8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:115 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_21_R1.fq.gz_G_to_A.fastq and zr3644_21_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1723:1000_1:N:0:NCATATCC+ATTGCACA/1 83 NC_047563.1_CT_converted 51129146 7 115M = 51129130 -131 TATGTGTAATTTATTTAAGGTTAATGGGGATAGTTTTATTTAATATTTATAAATTTTATGGAATTTGAAAAATTTTTTTATGAAGGATGGTGTATATTTGTTTTAGTGTGGGAAT FFF:F:FFF:FFF:FFFF,,FFFFFFF,,FFF,:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF:,FFFF:FFFFF:FFF:FFFFFFFF:::FFF AS:i:-12 XS:i:-24 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:85A21T7 YS:i:-6 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1723:1000_2:N:0:NCATATCC+ATTGCACA/2 163 NC_047563.1_CT_converted 51129130 7 115M = 51129146 131 AAAGAATAAATAATTATATGTGTAATTTATTTAAGGTTAATGGGGATAGTTTTATTTAATATTTATAAATTTTATGGAATTTGAAAAATTTTTTTATGAAGGATGGTGTATATTT FFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,::,FFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFF:F:FFFFF,:FF:FFFFFFFFFF AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:101A13 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_21_R1.fq.gz_C_to_T.fastq and zr3644_21_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1723:1000_1:N:0:NCATATCC+ATTGCACA/1 77 * 0 0 * * 0 0 ATTTTTATATTAAAATAAATATATATTATTTTTTATAAAAAAATTTTTTAAATTTTATAAAATTTATAAATATTAAATAAAATTATTTTTATTAATTTTAAATAAATTATATATA FFF:::FFFFFFFF:FFF:FFFFF:FFFF,:FF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:,FFF,,FFFFFFF,,FFFF:FFF:FFF:F:FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1723:1000_2:N:0:NCATATCC+ATTGCACA/2 141 * 0 0 * * 0 0 AAAAAATAAATAATTATATATATAATTTATTTAAAATTAATAAAAATAATTTTATTTAATATTTATAAATTTTATAAAATTTAAAAAATTTTTTTATAAAAAATAATATATATTT FFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,::,FFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFF:F:FFFFF,:FF:FFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_21_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_21_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:22290:29606_1:N:0:ACATATCC+ATTGCACA NW_022994881.1 520529 100000 reads; of these: 100000 (100.00%) were paired; of these: 72946 (72.95%) aligned concordantly 0 times 12160 (12.16%) aligned concordantly exactly 1 time 14894 (14.89%) aligned concordantly >1 times 27.05% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73046 (73.05%) aligned concordantly 0 times 12079 (12.08%) aligned concordantly exactly 1 time 14875 (14.88%) aligned concordantly >1 times 26.95% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73208 (73.21%) aligned concordantly 0 times 11987 (11.99%) aligned concordantly exactly 1 time 14805 (14.80%) aligned concordantly >1 times 26.79% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73133 (73.13%) aligned concordantly 0 times 12127 (12.13%) aligned concordantly exactly 1 time 14740 (14.74%) aligned concordantly >1 times 26.87% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_21_R1.fq.gz_C_to_T.fastq, zr3644_21_R1.fq.gz_G_to_A.fastq, zr3644_21_R2.fq.gz_C_to_T.fastq and zr3644_21_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61355 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 22075 Sequence pairs did not map uniquely: 16570 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15229 ((converted) top strand) GA/CT/CT: 15342 (complementary to (converted) top strand) GA/CT/GA: 15476 (complementary to (converted) bottom strand) CT/GA/GA: 15307 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2163758 Total methylated C's in CpG context: 28956 Total methylated C's in CHG context: 1733 Total methylated C's in CHH context: 7474 Total methylated C's in Unknown context: 76 Total unmethylated C's in CpG context: 250171 Total unmethylated C's in CHG context: 375364 Total unmethylated C's in CHH context: 1500060 Total unmethylated C's in Unknown context: 5000 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_22_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_22_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_22_R1.fq.gz Writing a C -> T converted version of the input file zr3644_22_R1.fq.gz to zr3644_22_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_22_R1.fq.gz to zr3644_22_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_22_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fq.gz Writing a C -> T converted version of the input file zr3644_22_R2.fq.gz to zr3644_22_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_22_R2.fq.gz to zr3644_22_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_22_R2.fq.gz (100001 sequences in total) Input files are zr3644_22_R1.fq.gz_C_to_T.fastq and zr3644_22_R1.fq.gz_G_to_A.fastq and zr3644_22_R2.fq.gz_C_to_T.fastq and zr3644_22_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_22_R1.fq.gz_C_to_T.fastq and zr3644_22_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2519:1000_1:N:0:NCATAGAT+CACCTTAA/1 77 * 0 0 * * 0 0 TTATATTATTAAATATTAAAAATTAATAAAATTTTAATTAAATTATTAATTTTATTATAAATAAATTAATATTAATAATAATATTAAAAATTTTTTATATTTTATTAATTAATTT FFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFF:F:F:FFFFFFFFFFFF,,FFF:F::,FF:,: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2519:1000_2:N:0:NCATAGAT+CACCTTAA/2 141 * 0 0 * * 0 0 ATTTTAATAATAATTTATATTAAAATTTAATAAAAAAAAATTAATAAATTAAAATTTAAAAATTTAAAATTTAAATTAATTTATATTATTTAAAATTTTTATATAAATAAAAATA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:F::FFFFFFF,:FFFFFFFFFFFFF:FFFFFFF:F:FFFFF:FFFFFF:FFFFFFF,FFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_22_R1.fq.gz_G_to_A.fastq and zr3644_22_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2519:1000_1:N:0:NCATAGAT+CACCTTAA/1 99 NC_047568.1_GA_converted 48583968 42 115M = 48584248 395 TTATACCATTAAATATTAAAAATTAATAAAATTCTAATTAAACCATCAATTTTACTATAAACAAATCAATATTAATAATAATATCAAAAATCTCTTATACCCCATTAATCAATTT FFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFF:F:F:FFFFFFFFFFFF,,FFF:F::,FF:,: AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:115 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2519:1000_2:N:0:NCATAGAT+CACCTTAA/2 147 NC_047568.1_GA_converted 48584248 42 115M = 48583968 -395 CACTTTTATCTATATAAAAATTTCAAATAACACAAATCAACCCAAATTTTAAATCCTCAAACCCTAATCTACCAACCTTTTCCTACTAAATTTTAACATAAACTATTATCAAAAT FFF:FFFFFFFF,FFFFFFF:FFFFFF:FFFFF:F:FFFFFFF:FFFFFFFFFFFFF:,FFFFFFF::F:FFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:115 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_22_R1.fq.gz_G_to_A.fastq and zr3644_22_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2519:1000_1:N:0:NCATAGAT+CACCTTAA/1 77 * 0 0 * * 0 0 TTATACCATTAAATATTAAAAATTAATAAAATTCTAATTAAACCATCAATTTTACTATAAACAAATCAATATTAATAATAATATCAAAAATCTCTTATACCCCATTAATCAATTT FFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFF:F:F:FFFFFFFFFFFF,,FFF:F::,FF:,: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2519:1000_2:N:0:NCATAGAT+CACCTTAA/2 141 * 0 0 * * 0 0 ATTTTGATAATAGTTTATGTTAAAATTTAGTAGGAAAAGGTTGGTAGATTAGGGTTTGAGGATTTAAAATTTGGGTTGATTTGTGTTATTTGAAATTTTTATATAGATAAAAGTG FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:F::FFFFFFF,:FFFFFFFFFFFFF:FFFFFFF:F:FFFFF:FFFFFF:FFFFFFF,FFFFFFFF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_22_R1.fq.gz_C_to_T.fastq and zr3644_22_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2519:1000_1:N:0:NCATAGAT+CACCTTAA/1 77 * 0 0 * * 0 0 TTATATTATTAAATATTAAAAATTAATAAAATTTTAATTAAATTATTAATTTTATTATAAATAAATTAATATTAATAATAATATTAAAAATTTTTTATATTTTATTAATTAATTT FFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFF:F:F:FFFFFFFFFFFF,,FFF:F::,FF:,: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2519:1000_2:N:0:NCATAGAT+CACCTTAA/2 141 * 0 0 * * 0 0 ATTTTAATAATAATTTATATTAAAATTTAATAAAAAAAAATTAATAAATTAAAATTTAAAAATTTAAAATTTAAATTAATTTATATTATTTAAAATTTTTATATAAATAAAAATA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:F::FFFFFFF,:FFFFFFFFFFFFF:FFFFFFF:F:FFFFF:FFFFFF:FFFFFFF,FFFFFFFF:FFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_22_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_22_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1101:4309:8860_1:N:0:TCATAGAT+CACCTTAA NW_022994946.1 2 100000 reads; of these: 100000 (100.00%) were paired; of these: 72729 (72.73%) aligned concordantly 0 times 12218 (12.22%) aligned concordantly exactly 1 time 15053 (15.05%) aligned concordantly >1 times 27.27% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72898 (72.90%) aligned concordantly 0 times 12360 (12.36%) aligned concordantly exactly 1 time 14742 (14.74%) aligned concordantly >1 times 27.10% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73168 (73.17%) aligned concordantly 0 times 12099 (12.10%) aligned concordantly exactly 1 time 14733 (14.73%) aligned concordantly >1 times 26.83% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72742 (72.74%) aligned concordantly 0 times 12345 (12.35%) aligned concordantly exactly 1 time 14913 (14.91%) aligned concordantly >1 times 27.26% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_22_R1.fq.gz_C_to_T.fastq, zr3644_22_R1.fq.gz_G_to_A.fastq, zr3644_22_R2.fq.gz_C_to_T.fastq and zr3644_22_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61839 Mapping efficiency: 61.8% Sequence pairs with no alignments under any condition: 21374 Sequence pairs did not map uniquely: 16787 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15348 ((converted) top strand) GA/CT/CT: 15517 (complementary to (converted) top strand) GA/CT/GA: 15496 (complementary to (converted) bottom strand) CT/GA/GA: 15477 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2188868 Total methylated C's in CpG context: 28781 Total methylated C's in CHG context: 1882 Total methylated C's in CHH context: 7621 Total methylated C's in Unknown context: 56 Total unmethylated C's in CpG context: 255932 Total unmethylated C's in CHG context: 381185 Total unmethylated C's in CHH context: 1513467 Total unmethylated C's in Unknown context: 5344 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.0% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_23_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_23_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_23_R1.fq.gz Writing a C -> T converted version of the input file zr3644_23_R1.fq.gz to zr3644_23_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_23_R1.fq.gz to zr3644_23_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_23_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fq.gz Writing a C -> T converted version of the input file zr3644_23_R2.fq.gz to zr3644_23_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_23_R2.fq.gz to zr3644_23_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_23_R2.fq.gz (100001 sequences in total) Input files are zr3644_23_R1.fq.gz_C_to_T.fastq and zr3644_23_R1.fq.gz_G_to_A.fastq and zr3644_23_R2.fq.gz_C_to_T.fastq and zr3644_23_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_23_R1.fq.gz_C_to_T.fastq and zr3644_23_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3206:1000_1:N:0:NTATTCCA+TTGTCTAC/1 99 NC_047564.1_CT_converted 52276293 40 33M1I81M = 52276308 127 AGTAGAAATAATTTATGGGGGAGTTAATGATGGAAAAAATGTTTATTGGGTATTTTAGAGATAGTATAGAAATTAATTTAATTAGTTTTAATATATATTGTTTATTAAAAATAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:F:FFFFFF AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:114 YS:i:-26 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:3206:1000_2:N:0:NTATTCCA+TTGTCTAC/2 147 NC_047564.1_CT_converted 52276308 40 18M1I94M = 52276293 -127 TGGGGTAGTTAAAGATGGAAAAAATGTTTATTGGGTATATTAGAGATAGTATAGAAATTAATTTAATTAGTTTTAATATATATTGTTTATTAAAAATAATAGAGATAGTTATT ,:F,,,F,,,FF,:F,,,FFFFFF,,,:,F,,,,,,:,,:,F:F,F,F,,F:F,FFF::FFF,FFF:FF:,:::FF:FFFFF,F:,F,FF:FFFFFFFFFFFF:F:F:::F:, AS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:5G6T24T74 YS:i:-8 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_23_R1.fq.gz_G_to_A.fastq and zr3644_23_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3206:1000_1:N:0:NTATTCCA+TTGTCTAC/1 77 * 0 0 * * 0 0 AATAAAAATAATTTATAAAAAAATTAATAATAAAAAAAATATTTATTAAATATTTTAAAAATAATATAAAAATTAATTTAATTAATTTTAATATATATTATTTATTAAAAATAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:F:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3206:1000_2:N:0:NTATTCCA+TTGTCTAC/2 141 * 0 0 * * 0 0 AATAATTATTTTTATTATTTTTAATAAATAATATATATTAAAATTAATTAAATTAATTTTTATATTATTTTTAATATATTTAATAAATATTTTTTTTATTTTTAATTGTTTTA ,:F:::F:F:FFFFFFFFFFFF:FF,F,:F,FFFFF:FF:::,:FF:FFF,FFF::FFF,F:F,,F,F,F:F,:,,:,,,,,,F,:,,,FFFFFF,,,F:,FF,,,F,,,F:, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_23_R1.fq.gz_G_to_A.fastq and zr3644_23_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3206:1000_1:N:0:NTATTCCA+TTGTCTAC/1 77 * 0 0 * * 0 0 AATAAAAATAATTTATAAAAAAATTAATAATAAAAAAAATATTTATTAAATATTTTAAAAATAATATAAAAATTAATTTAATTAATTTTAATATATATTATTTATTAAAAATAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:F:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3206:1000_2:N:0:NTATTCCA+TTGTCTAC/2 141 * 0 0 * * 0 0 AATAATTATTTTTATTATTTTTAATAAATAATATATATTAAAATTAATTAAATTAATTTTTATATTATTTTTAATATATTTAATAAATATTTTTTTTATTTTTAATTGTTTTA ,:F:::F:F:FFFFFFFFFFFF:FF,F,:F,FFFFF:FF:::,:FF:FFF,FFF::FFF,F:F,,F,F,F:F,:,,:,,,,,,F,:,,,FFFFFF,,,F:,FF,,,F,,,F:, YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_23_R1.fq.gz_C_to_T.fastq and zr3644_23_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3206:1000_1:N:0:NTATTCCA+TTGTCTAC/1 77 * 0 0 * * 0 0 AGTAGAAATAATTTATGGGGGAGTTAATGATGGAAAAAATGTTTATTGGGTATTTTAGAGATAGTATAGAAATTAATTTAATTAGTTTTAATATATATTGTTTATTAAAAATAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:F:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3206:1000_2:N:0:NTATTCCA+TTGTCTAC/2 141 * 0 0 * * 0 0 AATAACTATCTCTATTATTTTTAATAAACAATATATATTAAAACTAATTAAATTAATTTCTATACTATCTCTAATATACCCAATAAACATTTTTTCCATCTTTAACTACCCCA ,:F:::F:F:FFFFFFFFFFFF:FF,F,:F,FFFFF:FF:::,:FF:FFF,FFF::FFF,F:F,,F,F,F:F,:,,:,,,,,,F,:,,,FFFFFF,,,F:,FF,,,F,,,F:, YT:Z:UP >>> Writing bisulfite mapping results to zr3644_23_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_23_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72329 (72.33%) aligned concordantly 0 times 12421 (12.42%) aligned concordantly exactly 1 time 15250 (15.25%) aligned concordantly >1 times 27.67% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72899 (72.90%) aligned concordantly 0 times 11943 (11.94%) aligned concordantly exactly 1 time 15158 (15.16%) aligned concordantly >1 times 27.10% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72592 (72.59%) aligned concordantly 0 times 12213 (12.21%) aligned concordantly exactly 1 time 15195 (15.20%) aligned concordantly >1 times 27.41% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72822 (72.82%) aligned concordantly 0 times 11985 (11.98%) aligned concordantly exactly 1 time 15193 (15.19%) aligned concordantly >1 times 27.18% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_23_R1.fq.gz_C_to_T.fastq, zr3644_23_R1.fq.gz_G_to_A.fastq, zr3644_23_R2.fq.gz_C_to_T.fastq and zr3644_23_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61316 Mapping efficiency: 61.3% Sequence pairs with no alignments under any condition: 21132 Sequence pairs did not map uniquely: 17552 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15304 ((converted) top strand) GA/CT/CT: 15128 (complementary to (converted) top strand) GA/CT/GA: 15103 (complementary to (converted) bottom strand) CT/GA/GA: 15781 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2147258 Total methylated C's in CpG context: 28217 Total methylated C's in CHG context: 1894 Total methylated C's in CHH context: 7705 Total methylated C's in Unknown context: 40 Total unmethylated C's in CpG context: 251795 Total unmethylated C's in CHG context: 374551 Total unmethylated C's in CHH context: 1483096 Total unmethylated C's in Unknown context: 5236 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 0.8% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_24_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_24_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_24_R1.fq.gz Writing a C -> T converted version of the input file zr3644_24_R1.fq.gz to zr3644_24_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_24_R1.fq.gz to zr3644_24_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_24_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fq.gz Writing a C -> T converted version of the input file zr3644_24_R2.fq.gz to zr3644_24_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_24_R2.fq.gz to zr3644_24_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_24_R2.fq.gz (100001 sequences in total) Input files are zr3644_24_R1.fq.gz_C_to_T.fastq and zr3644_24_R1.fq.gz_G_to_A.fastq and zr3644_24_R2.fq.gz_C_to_T.fastq and zr3644_24_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_24_R1.fq.gz_C_to_T.fastq and zr3644_24_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:28275:1642_1:N:0:CCTCCGTC+CACCGATG/1 99 NW_022994860.1_CT_converted 133738 6 115M = 133744 121 TGATTAAATATTAATTGTTTATAATAGTAGTAATATTTAAAATTTGAATTATTTTAAAGGTGGTGTTTGGTGTGGAGTTGTAATAATGTTGATGGTTAAAGTTATGTGTGGGGAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFF:FFFFFFFFF:FFF,F,FFFFFFFFF:FFFFF:FFFFFFFFFFFF AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:76A8G17G11 YS:i:-18 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:28275:1642_2:N:0:CCTCCGTC+CACCGATG/2 147 NW_022994860.1_CT_converted 133744 6 115M = 133738 -121 AATATTAATTGTTTATAATAGTAGTAATATTTAAAATTTGAATTATTTTAAAGGTGGTGTTTGGTGTGGAGTTGTAATAATGTTGATGGTTAAAGTTATGTGTGGGGATGATGTA :FFFFFFFFFF,FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:70A8G17G17 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_24_R1.fq.gz_G_to_A.fastq and zr3644_24_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:28275:1642_1:N:0:CCTCCGTC+CACCGATG/1 77 * 0 0 * * 0 0 TAATTAAATATTAATTATTTATAATAATAATAATATTTAAAATTTAAATTATTTTAAAAATAATATTTAATATAAAATTATAATAATATTAATAATTAAAATTATATATAAAAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFF:FFFFFFFFF:FFF,F,FFFFFFFFF:FFFFF:FFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:28275:1642_2:N:0:CCTCCGTC+CACCGATG/2 141 * 0 0 * * 0 0 TATATTATTTTTATATATAATTTTAATTATTAATATTATTATAATTTTATATTAAATATTATTTTTAAAATAATTTAAATTTTAAATATTATTATTATTATAAATAATTAATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_24_R1.fq.gz_G_to_A.fastq and zr3644_24_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:28275:1642_1:N:0:CCTCCGTC+CACCGATG/1 77 * 0 0 * * 0 0 TAATTAAATATTAATTATTTATAATAATAATAATATTTAAAATTTAAATTATTTTAAAAATAATATTTAATATAAAATTATAATAATATTAATAATTAAAATTATATATAAAAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFF:FFFFFFFFF:FFF,F,FFFFFFFFF:FFFFF:FFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:28275:1642_2:N:0:CCTCCGTC+CACCGATG/2 141 * 0 0 * * 0 0 TATATTATTTTTATATATAATTTTAATTATTAATATTATTATAATTTTATATTAAATATTATTTTTAAAATAATTTAAATTTTAAATATTATTATTATTATAAATAATTAATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_24_R1.fq.gz_C_to_T.fastq and zr3644_24_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:28275:1642_1:N:0:CCTCCGTC+CACCGATG/1 83 NC_047561.1_GA_converted 15953605 6 115M = 15953599 -121 ATCCCCACACATAACTTTAACCATCAACATTATTACAACTCCACACCAAACACCACCTTTAAAATAATTCAAATTTTAAATATTACTACTATTATAAACAATTAATATTTAATCA FFFFFFFFFFFF:FFFFF:FFFFFFFFF,F,FFF:FFFFFFFFF:FFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:11C17C8T76 YS:i:-18 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:28275:1642_2:N:0:CCTCCGTC+CACCGATG/2 163 NC_047561.1_GA_converted 15953599 6 115M = 15953605 121 TACATCATCCCCACACATAACTTTAACCATCAACATTATTACAACTCCACACCAAACACCACCTTTAAAATAATTCAAATTTTAAATATTACTACTATTATAAACAATTAATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF,FFFFFFFFFF: AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:17C17C8T70 YS:i:-18 YT:Z:CP >>> Writing bisulfite mapping results to zr3644_24_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_24_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72667 (72.67%) aligned concordantly 0 times 12499 (12.50%) aligned concordantly exactly 1 time 14834 (14.83%) aligned concordantly >1 times 27.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72877 (72.88%) aligned concordantly 0 times 12157 (12.16%) aligned concordantly exactly 1 time 14966 (14.97%) aligned concordantly >1 times 27.12% overall alignment rate 100000 reads; of these: 100000 reads; of these:100000 ( 100000 (100.00100.00%%) were paired; of these:) were paired; of these: 7267673038 ( (72.6873.04%%) aligned concordantly 0 times) aligned concordantly 0 times 1246712142 ( (12.4712.14%%) aligned concordantly exactly 1 time) aligned concordantly exactly 1 time 1485714820 ( (14.8614.82%%) aligned concordantly >1 times) aligned concordantly >1 times 27.3226.96%% overall alignment rate overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_24_R1.fq.gz_C_to_T.fastq, zr3644_24_R1.fq.gz_G_to_A.fastq, zr3644_24_R2.fq.gz_C_to_T.fastq and zr3644_24_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 62315 Mapping efficiency: 62.3% Sequence pairs with no alignments under any condition: 21022 Sequence pairs did not map uniquely: 16663 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15540 ((converted) top strand) GA/CT/CT: 15661 (complementary to (converted) top strand) GA/CT/GA: 15398 (complementary to (converted) bottom strand) CT/GA/GA: 15716 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2207527 Total methylated C's in CpG context: 29017 Total methylated C's in CHG context: 1829 Total methylated C's in CHH context: 7614 Total methylated C's in Unknown context: 66 Total unmethylated C's in CpG context: 258161 Total unmethylated C's in CHG context: 383928 Total unmethylated C's in CHH context: 1526978 Total unmethylated C's in Unknown context: 5334 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.2% Bismark completed in 0d 0h 0m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fq.gz Writing a C -> T converted version of the input file zr3644_2_R1.fq.gz to zr3644_2_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_2_R1.fq.gz to zr3644_2_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_2_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fq.gz Writing a C -> T converted version of the input file zr3644_2_R2.fq.gz to zr3644_2_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_2_R2.fq.gz to zr3644_2_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_2_R2.fq.gz (100001 sequences in total) Input files are zr3644_2_R1.fq.gz_C_to_T.fastq and zr3644_2_R1.fq.gz_G_to_A.fastq and zr3644_2_R2.fq.gz_C_to_T.fastq and zr3644_2_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_2_R1.fq.gz_C_to_T.fastq and zr3644_2_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2013:1000_1:N:0:NTCATAAG+CCTTCTAA/1 77 * 0 0 * * 0 0 AATATAAATTAATTTTTTAAAAAAAATTTTATTTTAATTATATTATATAAAATATTATATTTTTATTAAATTAATTTAATTTTTTATTAATTATATAAATTTAATTTTTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFF,FFFFFFFFF:FFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2013:1000_2:N:0:NTCATAAG+CCTTCTAA/2 141 * 0 0 * * 0 0 ATATTTAAATTTTTATATTTAATAAAAATTAAATTTTAAAATTATTTAATTAATTTTTAAAAAAAATTAAATTTATATAATTAATAAAAAATTAAATTAATTTAATAAAAATATA FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_2_R1.fq.gz_G_to_A.fastq and zr3644_2_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2013:1000_1:N:0:NTCATAAG+CCTTCTAA/1 99 NC_047565.1_GA_converted 14478947 0 115M = 14479181 349 AATATAAACCAACCCCTTAAAAAAAATCCCATTTTAACTATATTATACAAAATATCACATTTTCACCAAACTAACTTAACCTCTTACTAACCATATAAACCCAATTCCTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFF,FFFFFFFFF:FFFFFFFFFF AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:74T1A14T23 YS:i:-54 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2013:1000_2:N:0:NTCATAAG+CCTTCTAA/2 147 NC_047565.1_GA_converted 14479181 0 115M = 14478947 -349 CACATTTTCACCAAACTAACTTAACCTCTTACTAACCATATAAACCCAATTCCTTTTAAAAATCAACTAAACAATCCCAAAACCCAATTCTCACTAAATATAAAAATCCAAATAT FFFFFFFFFF:FFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:F:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-54 XS:i:-42 XN:i:0 XM:i:9 XO:i:0 XG:i:0 NM:i:9 MD:Z:2T5T12A7A6T14T33C2C5C20 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_2_R1.fq.gz_G_to_A.fastq and zr3644_2_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2013:1000_1:N:0:NTCATAAG+CCTTCTAA/1 83 NC_047568.1_CT_converted 12200909 2 115M = 12200675 -349 TTTAAAAGGAATTGGGTTTATATGGTTAGTAAGAGGTTAAGTTAGTTTGGTGAAAATGTGATATTTTGTATAATATAGTTAAAATGGGATTTTTTTTAAGGGGTTGGTTTATATT FFFFFFFFFF:FFFFFFFFF,FFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:108G6 YS:i:-48 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2013:1000_2:N:0:NTCATAAG+CCTTCTAA/2 163 NC_047568.1_CT_converted 12200675 2 115M = 12200909 349 ATATTTGGATTTTTATATTTAGTGAGAATTGGGTTTTGGGATTGTTTAGTTGATTTTTAAAAGGAATTGGGTTTATATGGTTAGTAAGAGGTTAAGTTAGTTTGGTGAAAATGTG FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFF:FFFFFFFFFF AS:i:-48 XS:i:-58 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:14T11G2G33A2A11A8A5T21 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_2_R1.fq.gz_C_to_T.fastq and zr3644_2_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2013:1000_1:N:0:NTCATAAG+CCTTCTAA/1 77 * 0 0 * * 0 0 AATATAAATTAATTTTTTAAAAAAAATTTTATTTTAATTATATTATATAAAATATTATATTTTTATTAAATTAATTTAATTTTTTATTAATTATATAAATTTAATTTTTTTTAAA FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFF,FFFFFFFFF:FFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2013:1000_2:N:0:NTCATAAG+CCTTCTAA/2 141 * 0 0 * * 0 0 ATATTTAAATTTTTATATTTAATAAAAATTAAATTTTAAAATTATTTAATTAATTTTTAAAAAAAATTAAATTTATATAATTAATAAAAAATTAAATTAATTTAATAAAAATATA FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFF:FFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_2_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73117 (73.12%) aligned concordantly 0 times 12076 (12.08%) aligned concordantly exactly 1 time 14807 (14.81%) aligned concordantly >1 times 26.88% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73278 (73.28%) aligned concordantly 0 times 12041 (12.04%) aligned concordantly exactly 1 time 14681 (14.68%) aligned concordantly >1 times 26.72% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73353 (73.35%) aligned concordantly 0 times 12020 (12.02%) aligned concordantly exactly 1 time 14627 (14.63%) aligned concordantly >1 times 26.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73184 (73.18%) aligned concordantly 0 times 12163 (12.16%) aligned concordantly exactly 1 time 14653 (14.65%) aligned concordantly >1 times 26.82% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_2_R1.fq.gz_C_to_T.fastq, zr3644_2_R1.fq.gz_G_to_A.fastq, zr3644_2_R2.fq.gz_C_to_T.fastq and zr3644_2_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61033 Mapping efficiency: 61.0% Sequence pairs with no alignments under any condition: 22427 Sequence pairs did not map uniquely: 16540 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15101 ((converted) top strand) GA/CT/CT: 15016 (complementary to (converted) top strand) GA/CT/GA: 15459 (complementary to (converted) bottom strand) CT/GA/GA: 15457 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2176242 Total methylated C's in CpG context: 28402 Total methylated C's in CHG context: 1868 Total methylated C's in CHH context: 7614 Total methylated C's in Unknown context: 76 Total unmethylated C's in CpG context: 251780 Total unmethylated C's in CHG context: 374557 Total unmethylated C's in CHH context: 1512021 Total unmethylated C's in Unknown context: 5381 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_3_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_3_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_3_R1.fq.gz Writing a C -> T converted version of the input file zr3644_3_R1.fq.gz to zr3644_3_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_3_R1.fq.gz to zr3644_3_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_3_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fq.gz Writing a C -> T converted version of the input file zr3644_3_R2.fq.gz to zr3644_3_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_3_R2.fq.gz to zr3644_3_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_3_R2.fq.gz (100001 sequences in total) Input files are zr3644_3_R1.fq.gz_C_to_T.fastq and zr3644_3_R1.fq.gz_G_to_A.fastq and zr3644_3_R2.fq.gz_C_to_T.fastq and zr3644_3_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_3_R1.fq.gz_C_to_T.fastq and zr3644_3_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2121:1000_1:N:0:NTCTGCAG+TACATCCA/1 99 NC_047561.1_CT_converted 49664063 23 52M1D30M1D33M = 49664071 124 TTAAAAATGAAAAGAATGTATGGATTTTGAATAGAATTAGTTTTAGGATTTATTTTTTTTTTTAGTTTTTAAATATTGAGGGGTTTTATTTATGTATGTGAATTAATTTTAATGA FFFF,FFF:FFF,F:FFF,FFF::FFF,,,FFFFF:FF,FFFFFF:FFFFF:FFF:FFFFF,FF:::FFF,FFF,FFF,FFFFFFF,,,FF,,F,FF,FF,FFFFF:FFFF,F,F AS:i:-34 XN:i:0 XM:i:3 XO:i:2 XG:i:2 NM:i:5 MD:Z:52^T30^T0T4T4G22 YS:i:-22 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2121:1000_2:N:0:NTCTGCAG+TACATCCA/2 147 NC_047561.1_CT_converted 49664071 23 44M1D30M1D40M = 49664063 -124 GAAAAGAATGTATGGATTTTGAATAGAATTAGTTTTAGGATTTATTTTTTTTTTTAGTTTTTAAATATTGAGGGGTTTTTTTTAGGTATGTGAATTAATTTTAATGAATAAAAA FF:,F,,,,,,,FF:F::FF:,:FFFF::F,FF,FFF,:F::F:FF:FFFF:,F:FFFFF:FFF:F,F:F,FFFFFFFFF,FFFFF,FFFFFFFFFFFFFFFFFFF,FFFFFFF AS:i:-22 XN:i:0 XM:i:1 XO:i:2 XG:i:2 NM:i:3 MD:Z:44^T30^T0T39 YS:i:-34 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_3_R1.fq.gz_G_to_A.fastq and zr3644_3_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2121:1000_1:N:0:NTCTGCAG+TACATCCA/1 77 * 0 0 * * 0 0 TTAAAAATAAAAAAAATATATAAATTTTAAATAAAATTAATTTTAAAATTTATTTTTTTTTTTAATTTTTAAATATTAAAAAATTTTATTTATATATATAAATTAATTTTAATAA FFFF,FFF:FFF,F:FFF,FFF::FFF,,,FFFFF:FF,FFFFFF:FFFFF:FFF:FFFFF,FF:::FFF,FFF,FFF,FFFFFFF,,,FF,,F,FF,FF,FFFFF:FFFF,F,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2121:1000_2:N:0:NTCTGCAG+TACATCCA/2 141 * 0 0 * * 0 0 TTTTTATTTATTAAAATTAATTTATATATTTAAAAAAAATTTTTTAATATTTAAAAATTAAAAAAAAAAATAAATTTTAAAATTAATTTTATTTAAAATTTATATATTTTTTTT FFFFFFF,FFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFF,F:F,F:FFF:FFFFF:F,:FFFF:FF:F::F:,FFF,FF,F::FFFF:,:FF::F:FF,,,,,,,F,:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_3_R1.fq.gz_G_to_A.fastq and zr3644_3_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2121:1000_1:N:0:NTCTGCAG+TACATCCA/1 77 * 0 0 * * 0 0 TTAAAAATAAAAAAAATATATAAATTTTAAATAAAATTAATTTTAAAATTTATTTTTTTTTTTAATTTTTAAATATTAAAAAATTTTATTTATATATATAAATTAATTTTAATAA FFFF,FFF:FFF,F:FFF,FFF::FFF,,,FFFFF:FF,FFFFFF:FFFFF:FFF:FFFFF,FF:::FFF,FFF,FFF,FFFFFFF,,,FF,,F,FF,FF,FFFFF:FFFF,F,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2121:1000_2:N:0:NTCTGCAG+TACATCCA/2 141 * 0 0 * * 0 0 TTTTTATTTATTAAAATTAATTTATATATTTAAAAAAAATTTTTTAATATTTAAAAATTAAAAAAAAAAATAAATTTTAAAATTAATTTTATTTAAAATTTATATATTTTTTTT FFFFFFF,FFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFF,F:F,F:FFF:FFFFF:F,:FFFF:FF:F::F:,FFF,FF,F::FFFF:,:FF::F:FF,,,,,,,F,:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_3_R1.fq.gz_C_to_T.fastq and zr3644_3_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2121:1000_1:N:0:NTCTGCAG+TACATCCA/1 77 * 0 0 * * 0 0 TTAAAAATGAAAAGAATGTATGGATTTTGAATAGAATTAGTTTTAGGATTTATTTTTTTTTTTAGTTTTTAAATATTGAGGGGTTTTATTTATGTATGTGAATTAATTTTAATGA FFFF,FFF:FFF,F:FFF,FFF::FFF,,,FFFFF:FF,FFFFFF:FFFFF:FFF:FFFFF,FF:::FFF,FFF,FFF,FFFFFFF,,,FF,,F,FF,FF,FFFFF:FFFF,F,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2121:1000_2:N:0:NTCTGCAG+TACATCCA/2 141 * 0 0 * * 0 0 TTTTTATTCATTAAAATTAATTCACATACCTAAAAAAAACCCCTCAATATTTAAAAACTAAAAAAAAAAATAAATCCTAAAACTAATTCTATTCAAAATCCATACATTCTTTTC FFFFFFF,FFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFF,F:F,F:FFF:FFFFF:F,:FFFF:FF:F::F:,FFF,FF,F::FFFF:,:FF::F:FF,,,,,,,F,:FF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_3_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_3_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72941 (72.94%) aligned concordantly 0 times 12092 (12.09%) aligned concordantly exactly 1 time 14967 (14.97%) aligned concordantly >1 times 27.06% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72689 (72.69%) aligned concordantly 0 times 12177 (12.18%) aligned concordantly exactly 1 time 15134 (15.13%) aligned concordantly >1 times 27.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73188 (73.19%) aligned concordantly 0 times 11918 (11.92%) aligned concordantly exactly 1 time 14894 (14.89%) aligned concordantly >1 times 26.81% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72744 (72.74%) aligned concordantly 0 times 12084 (12.08%) aligned concordantly exactly 1 time 15172 (15.17%) aligned concordantly >1 times 27.26% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_3_R1.fq.gz_C_to_T.fastq, zr3644_3_R1.fq.gz_G_to_A.fastq, zr3644_3_R2.fq.gz_C_to_T.fastq and zr3644_3_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61161 Mapping efficiency: 61.2% Sequence pairs with no alignments under any condition: 21806 Sequence pairs did not map uniquely: 17033 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15370 ((converted) top strand) GA/CT/CT: 15366 (complementary to (converted) top strand) GA/CT/GA: 15264 (complementary to (converted) bottom strand) CT/GA/GA: 15161 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2154532 Total methylated C's in CpG context: 28478 Total methylated C's in CHG context: 1768 Total methylated C's in CHH context: 7387 Total methylated C's in Unknown context: 62 Total unmethylated C's in CpG context: 250025 Total unmethylated C's in CHG context: 372477 Total unmethylated C's in CHH context: 1494397 Total unmethylated C's in Unknown context: 5422 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_4_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_4_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_4_R1.fq.gz Writing a C -> T converted version of the input file zr3644_4_R1.fq.gz to zr3644_4_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_4_R1.fq.gz to zr3644_4_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_4_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fq.gz Writing a C -> T converted version of the input file zr3644_4_R2.fq.gz to zr3644_4_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_4_R2.fq.gz to zr3644_4_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_4_R2.fq.gz (100001 sequences in total) Input files are zr3644_4_R1.fq.gz_C_to_T.fastq and zr3644_4_R1.fq.gz_G_to_A.fastq and zr3644_4_R2.fq.gz_C_to_T.fastq and zr3644_4_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_4_R1.fq.gz_C_to_T.fastq and zr3644_4_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1868:1000_1:N:0:NTGACTCT+TGACGGCC/1 99 NC_047566.1_CT_converted 9989017 1 83M = 9989007 -93 TTTGAGGTAAATAAAGAGGTGATATTAGTAGTAAATTGTATGAAGAATTTAATGGTATTAATTGTTTTTATAGAATTTGTGTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:83 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1868:1000_2:N:0:NTGACTCT+TGACGGCC/2 147 NC_047566.1_CT_converted 9989007 1 83M = 9989017 93 TTGGAGAAAGTTTGAGGTAAATAAAGAGGTGATATTAGTAGTAAATTGTATGAAGAATTTAATGGTATTAATTGTTTTTATAG FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:83 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_4_R1.fq.gz_G_to_A.fastq and zr3644_4_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1868:1000_1:N:0:NTGACTCT+TGACGGCC/1 77 * 0 0 * * 0 0 TTTAAAATAAATAAAAAAATAATATTAATAATAAATTATATAAAAAATTTAATAATATTAATTATTTTTATAAAATTTATATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1868:1000_2:N:0:NTGACTCT+TGACGGCC/2 141 * 0 0 * * 0 0 TTATAAAAATAATTAATATTATTAAATTTTTTATATAATTTATTATTAATATTATTTTTTTATTTATTTTAAATTTTTTTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_4_R1.fq.gz_G_to_A.fastq and zr3644_4_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1868:1000_1:N:0:NTGACTCT+TGACGGCC/1 77 * 0 0 * * 0 0 TTTAAAATAAATAAAAAAATAATATTAATAATAAATTATATAAAAAATTTAATAATATTAATTATTTTTATAAAATTTATATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1868:1000_2:N:0:NTGACTCT+TGACGGCC/2 141 * 0 0 * * 0 0 TTATAAAAATAATTAATATTATTAAATTTTTTATATAATTTATTATTAATATTATTTTTTTATTTATTTTAAATTTTTTTTAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_4_R1.fq.gz_C_to_T.fastq and zr3644_4_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1868:1000_1:N:0:NTGACTCT+TGACGGCC/1 83 NC_047562.1_GA_converted 5038905 1 83M = 5038915 93 TACACAAATTCTATAAAAACAATTAATACCATTAAATTCTTCATACAATTTACTACTAATATCACCTCTTTATTTACCTCAAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:83 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1868:1000_2:N:0:NTGACTCT+TGACGGCC/2 163 NC_047562.1_GA_converted 5038915 1 83M = 5038905 -93 CTATAAAAACAATTAATACCATTAAATTCTTCATACAATTTACTACTAATATCACCTCTTTATTTACCTCAAACTTTCTCCAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:83 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to zr3644_4_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_4_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72792 (72.79%) aligned concordantly 0 times 11987 (11.99%) aligned concordantly exactly 1 time 15221 (15.22%) aligned concordantly >1 times 27.21% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73089 (73.09%) aligned concordantly 0 times 11996 (12.00%) aligned concordantly exactly 1 time 14915 (14.91%) aligned concordantly >1 times 26.91% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73158 (73.16%) aligned concordantly 0 times 12016 (12.02%) aligned concordantly exactly 1 time 14826 (14.83%) aligned concordantly >1 times 26.84% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72718 (72.72%) aligned concordantly 0 times 12075 (12.07%) aligned concordantly exactly 1 time 15207 (15.21%) aligned concordantly >1 times 27.28% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_4_R1.fq.gz_C_to_T.fastq, zr3644_4_R1.fq.gz_G_to_A.fastq, zr3644_4_R2.fq.gz_C_to_T.fastq and zr3644_4_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61250 Mapping efficiency: 61.2% Sequence pairs with no alignments under any condition: 21911 Sequence pairs did not map uniquely: 16839 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15247 ((converted) top strand) GA/CT/CT: 15316 (complementary to (converted) top strand) GA/CT/GA: 15277 (complementary to (converted) bottom strand) CT/GA/GA: 15410 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2157029 Total methylated C's in CpG context: 28381 Total methylated C's in CHG context: 1690 Total methylated C's in CHH context: 7022 Total methylated C's in Unknown context: 85 Total unmethylated C's in CpG context: 246166 Total unmethylated C's in CHG context: 369285 Total unmethylated C's in CHH context: 1504485 Total unmethylated C's in Unknown context: 5278 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_5_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_5_R1.fq.gz Writing a C -> T converted version of the input file zr3644_5_R1.fq.gz to zr3644_5_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_5_R1.fq.gz to zr3644_5_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_5_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fq.gz Writing a C -> T converted version of the input file zr3644_5_R2.fq.gz to zr3644_5_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_5_R2.fq.gz to zr3644_5_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_5_R2.fq.gz (100001 sequences in total) Input files are zr3644_5_R1.fq.gz_C_to_T.fastq and zr3644_5_R1.fq.gz_G_to_A.fastq and zr3644_5_R2.fq.gz_C_to_T.fastq and zr3644_5_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_5_R1.fq.gz_C_to_T.fastq and zr3644_5_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5267:1000_1:N:0:NCTGGTAT+GTAAGCAA/1 77 * 0 0 * * 0 0 TTAAATATATTTTTATTAATTAAAAAAAATAATAATAATATTTATTTAAATTAATTTTATTAAAATATATTAAATATATTAATATAAATTATATTAAAATTAAATTTTAATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5267:1000_2:N:0:NCTGGTAT+GTAAGCAA/2 141 * 0 0 * * 0 0 TATATTATAAAATAATATATATATAAAATAAATTAATTTATTTAATTTTAAATTTAAATTTTATATAAATTAATATTTTTAAATTATATAATATATTATATTTTTTAATTTTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_5_R1.fq.gz_G_to_A.fastq and zr3644_5_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5267:1000_1:N:0:NCTGGTAT+GTAAGCAA/1 77 * 0 0 * * 0 0 CTAAACACATCTCTATTAATCAAAAAAAATAATAATAATATCTATTTAAATTAATTTCACCAAAACATACTAAATACACCAATACAAATTACATCAAAATCAAATTTCAATCAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5267:1000_2:N:0:NCTGGTAT+GTAAGCAA/2 141 * 0 0 * * 0 0 TATGTTATAAAATGATGTGTGTGTGAGATGAATTAATTTGTTTGATTTTAGATTTAAATTTTGTATAAATTAATATTTTTAAATTATATAATATGTTATATTTTTTGATTTTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_5_R1.fq.gz_G_to_A.fastq and zr3644_5_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5267:1000_1:N:0:NCTGGTAT+GTAAGCAA/1 77 * 0 0 * * 0 0 CTAAACACATCTCTATTAATCAAAAAAAATAATAATAATATCTATTTAAATTAATTTCACCAAAACATACTAAATACACCAATACAAATTACATCAAAATCAAATTTCAATCAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5267:1000_2:N:0:NCTGGTAT+GTAAGCAA/2 141 * 0 0 * * 0 0 TATGTTATAAAATGATGTGTGTGTGAGATGAATTAATTTGTTTGATTTTAGATTTAAATTTTGTATAAATTAATATTTTTAAATTATATAATATGTTATATTTTTTGATTTTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_5_R1.fq.gz_C_to_T.fastq and zr3644_5_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5267:1000_1:N:0:NCTGGTAT+GTAAGCAA/1 77 * 0 0 * * 0 0 TTAAATATATTTTTATTAATTAAAAAAAATAATAATAATATTTATTTAAATTAATTTTATTAAAATATATTAAATATATTAATATAAATTATATTAAAATTAAATTTTAATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5267:1000_2:N:0:NCTGGTAT+GTAAGCAA/2 141 * 0 0 * * 0 0 TATATTATAAAATAATATATATATAAAATAAATTAATTTATTTAATTTTAAATTTAAATTTTATATAAATTAATATTTTTAAATTATATAATATATTATATTTTTTAATTTTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_5_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1101:9082:12931_1:N:0:TCTGGTAT+GTAAGCAA NC_001276.1 18130 100000 reads; of these: 100000 (100.00%) were paired; of these: 73113 (73.11%) aligned concordantly 0 times 11985 (11.98%) aligned concordantly exactly 1 time 14902 (14.90%) aligned concordantly >1 times 26.89% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72850 (72.85%) aligned concordantly 0 times 12083 (12.08%) aligned concordantly exactly 1 time 15067 (15.07%) aligned concordantly >1 times 27.15% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73118 (73.12%) aligned concordantly 0 times 12047 (12.05%) aligned concordantly exactly 1 time 14835 (14.84%) aligned concordantly >1 times 26.88% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72700 (72.70%) aligned concordantly 0 times 12292 (12.29%) aligned concordantly exactly 1 time 15008 (15.01%) aligned concordantly >1 times 27.30% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_5_R1.fq.gz_C_to_T.fastq, zr3644_5_R1.fq.gz_G_to_A.fastq, zr3644_5_R2.fq.gz_C_to_T.fastq and zr3644_5_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61443 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 21828 Sequence pairs did not map uniquely: 16729 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15233 ((converted) top strand) GA/CT/CT: 15534 (complementary to (converted) top strand) GA/CT/GA: 15404 (complementary to (converted) bottom strand) CT/GA/GA: 15271 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2175198 Total methylated C's in CpG context: 28268 Total methylated C's in CHG context: 1865 Total methylated C's in CHH context: 7941 Total methylated C's in Unknown context: 80 Total unmethylated C's in CpG context: 249908 Total unmethylated C's in CHG context: 375267 Total unmethylated C's in CHH context: 1511949 Total unmethylated C's in Unknown context: 5420 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_6_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_6_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_6_R1.fq.gz Writing a C -> T converted version of the input file zr3644_6_R1.fq.gz to zr3644_6_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_6_R1.fq.gz to zr3644_6_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_6_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fq.gz Writing a C -> T converted version of the input file zr3644_6_R2.fq.gz to zr3644_6_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_6_R2.fq.gz to zr3644_6_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_6_R2.fq.gz (100001 sequences in total) Input files are zr3644_6_R1.fq.gz_C_to_T.fastq and zr3644_6_R1.fq.gz_G_to_A.fastq and zr3644_6_R2.fq.gz_C_to_T.fastq and zr3644_6_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_6_R1.fq.gz_C_to_T.fastq and zr3644_6_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:16577:1642_1:N:0:CATTAGTG+TATGTAGT/1 77 * 0 0 * * 0 0 ATTTTTTTATTTTTATATTAATATTTTATATATTTTTAAAAAAATAAAAAAAAAAAAAAAATAATTTTATAATAATTTAATTTTTTATATATAATTTAAAAAAATTAATTATTAT FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFF:,,FFFFFF,FFF,FFF,FFFF:FFFFF:FF:FFFFFFFFFF:FFF:F,FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:16577:1642_2:N:0:CATTAGTG+TATGTAGT/2 141 * 0 0 * * 0 0 AAAAAAAAAATAAAAAAAATTATTTTTTTTTTTTTATTTTTTTTTTTATTAATAAATTTTTTTAAATTATAAAAAAAAAATTTAATTATTTATAAATATTTTTTTTTTTTTTTTT FFFFFFF,F,:,::F,F,FF:,F:FFF,:F::F:,,::F,F,FFFF,F,F:,,,FF,FFFF,:FFFF,,,:,:,FF:,FF,:,:,F:,F:,,F,:,:,FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_6_R1.fq.gz_G_to_A.fastq and zr3644_6_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:16577:1642_1:N:0:CATTAGTG+TATGTAGT/1 77 * 0 0 * * 0 0 ATTTCCTTATTTTCATATTAATATTTTACATACTCCCAAAAAAATAAAAAAAAAAAAAAAACAACTCCATAATAATTCAATTTTTTATATATAATTTAAAAAAATTAATTACTAC FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFF:,,FFFFFF,FFF,FFF,FFFF:FFFFF:FF:FFFFFFFFFF:FFF:F,FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:16577:1642_2:N:0:CATTAGTG+TATGTAGT/2 141 * 0 0 * * 0 0 GGGGGGGGGGTAAGGGGGGTTGTTTTTTTTTTTTTATTTTTTTTTTTATTAATAAATTTTTTTAAATTATAAAAAAAAAATTTAATTATTTATGAGTGTTTTTTTTTTTTTTTTT FFFFFFF,F,:,::F,F,FF:,F:FFF,:F::F:,,::F,F,FFFF,F,F:,,,FF,FFFF,:FFFF,,,:,:,FF:,FF,:,:,F:,F:,,F,:,:,FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_6_R1.fq.gz_G_to_A.fastq and zr3644_6_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:16577:1642_1:N:0:CATTAGTG+TATGTAGT/1 77 * 0 0 * * 0 0 ATTTCCTTATTTTCATATTAATATTTTACATACTCCCAAAAAAATAAAAAAAAAAAAAAAACAACTCCATAATAATTCAATTTTTTATATATAATTTAAAAAAATTAATTACTAC FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFF:,,FFFFFF,FFF,FFF,FFFF:FFFFF:FF:FFFFFFFFFF:FFF:F,FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:16577:1642_2:N:0:CATTAGTG+TATGTAGT/2 141 * 0 0 * * 0 0 GGGGGGGGGGTAAGGGGGGTTGTTTTTTTTTTTTTATTTTTTTTTTTATTAATAAATTTTTTTAAATTATAAAAAAAAAATTTAATTATTTATGAGTGTTTTTTTTTTTTTTTTT FFFFFFF,F,:,::F,F,FF:,F:FFF,:F::F:,,::F,F,FFFF,F,F:,,,FF,FFFF,:FFFF,,,:,:,FF:,FF,:,:,F:,F:,,F,:,:,FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_6_R1.fq.gz_C_to_T.fastq and zr3644_6_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:16577:1642_1:N:0:CATTAGTG+TATGTAGT/1 77 * 0 0 * * 0 0 ATTTTTTTATTTTTATATTAATATTTTATATATTTTTAAAAAAATAAAAAAAAAAAAAAAATAATTTTATAATAATTTAATTTTTTATATATAATTTAAAAAAATTAATTATTAT FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFFF:,,FFFFFF,FFF,FFF,FFFF:FFFFF:FF:FFFFFFFFFF:FFF:F,FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:16577:1642_2:N:0:CATTAGTG+TATGTAGT/2 141 * 0 0 * * 0 0 AAAAAAAAAATAAAAAAAATTATTTTTTTTTTTTTATTTTTTTTTTTATTAATAAATTTTTTTAAATTATAAAAAAAAAATTTAATTATTTATAAATATTTTTTTTTTTTTTTTT FFFFFFF,F,:,::F,F,FF:,F:FFF,:F::F:,,::F,F,FFFF,F,F:,,,FF,FFFF,:FFFF,,,:,:,FF:,FF,:,:,F:,F:,,F,:,:,FFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zr3644_6_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_6_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72771 (72.77%) aligned concordantly 0 times 12207 (12.21%) aligned concordantly exactly 1 time 15022 (15.02%) aligned concordantly >1 times 27.23% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72983 (72.98%) aligned concordantly 0 times 12247 (12.25%) aligned concordantly exactly 1 time 14770 (14.77%) aligned concordantly >1 times 27.02% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72769 (72.77%) aligned concordantly 0 times 12306 (12.31%) aligned concordantly exactly 1 time 14925 (14.93%) aligned concordantly >1 times 27.23% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73074 (73.07%) aligned concordantly 0 times 12082 (12.08%) aligned concordantly exactly 1 time 14844 (14.84%) aligned concordantly >1 times 26.93% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_6_R1.fq.gz_C_to_T.fastq, zr3644_6_R1.fq.gz_G_to_A.fastq, zr3644_6_R2.fq.gz_C_to_T.fastq and zr3644_6_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61890 Mapping efficiency: 61.9% Sequence pairs with no alignments under any condition: 21393 Sequence pairs did not map uniquely: 16717 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15418 ((converted) top strand) GA/CT/CT: 15575 (complementary to (converted) top strand) GA/CT/GA: 15425 (complementary to (converted) bottom strand) CT/GA/GA: 15472 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2177048 Total methylated C's in CpG context: 28799 Total methylated C's in CHG context: 1808 Total methylated C's in CHH context: 7682 Total methylated C's in Unknown context: 44 Total unmethylated C's in CpG context: 250643 Total unmethylated C's in CHG context: 374718 Total unmethylated C's in CHH context: 1513398 Total unmethylated C's in Unknown context: 5279 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 0.8% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_7_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_7_R1.fq.gz Writing a C -> T converted version of the input file zr3644_7_R1.fq.gz to zr3644_7_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_7_R1.fq.gz to zr3644_7_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_7_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fq.gz Writing a C -> T converted version of the input file zr3644_7_R2.fq.gz to zr3644_7_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_7_R2.fq.gz to zr3644_7_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_7_R2.fq.gz (100001 sequences in total) Input files are zr3644_7_R1.fq.gz_C_to_T.fastq and zr3644_7_R1.fq.gz_G_to_A.fastq and zr3644_7_R2.fq.gz_C_to_T.fastq and zr3644_7_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_7_R1.fq.gz_C_to_T.fastq and zr3644_7_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:19370:1407_1:N:0:ACGGTCAG+AACGAGGC/1 99 NC_047560.1_CT_converted 5405277 15 115M = 5405274 -118 GGATATTTTTATTTTAGTATTGAATGATATTAGAAATTTTAGGAGTTTAGATATGTAAAATATATTAATATATGTTGATAAAATTTATATTTAGATAAAATTGATAAAAAATGTA FFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFF:FFFFFF:FFFFF,FFFFFFFF:FFFFFFFFFF:F AS:i:-12 XS:i:-37 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:10G62A41 YS:i:-12 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:19370:1407_2:N:0:ACGGTCAG+AACGAGGC/2 147 NC_047560.1_CT_converted 5405274 15 115M = 5405277 118 AATGGATATTTTTATTTTAGTATTGAATGATATTAGAAATTTTAGGAGTTTAGATATGTAAAATATATTAATATATGTTGATAAAATTTATATTTAGATAAAATTGATAAAAAAT FFFF:FFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFF::FFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-12 XS:i:-31 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:13G62A38 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_7_R1.fq.gz_G_to_A.fastq and zr3644_7_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:19370:1407_1:N:0:ACGGTCAG+AACGAGGC/1 77 * 0 0 * * 0 0 AAATATTTTTATTTTAATATTAAATAATATTAAAAATTTTAAAAATTTAAATATATAAAATATATTAATATATATTAATAAAATTTATATTTAAATAAAATTAATAAAAAATATA FFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFF:FFFFFF:FFFFF,FFFFFFFF:FFFFFFFFFF:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:19370:1407_2:N:0:ACGGTCAG+AACGAGGC/2 141 * 0 0 * * 0 0 ATTTTTTATTAATTTTATTTAAATATAAATTTTATTAATATATATTAATATATTTTATATATTTAAATTTTTAAAATTTTTAATATTATTTAATATTAAAATAAAAATATTTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF::FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_7_R1.fq.gz_G_to_A.fastq and zr3644_7_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:19370:1407_1:N:0:ACGGTCAG+AACGAGGC/1 77 * 0 0 * * 0 0 AAATATTTTTATTTTAATATTAAATAATATTAAAAATTTTAAAAATTTAAATATATAAAATATATTAATATATATTAATAAAATTTATATTTAAATAAAATTAATAAAAAATATA FFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFF:FFFFFF:FFFFF,FFFFFFFF:FFFFFFFFFF:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:19370:1407_2:N:0:ACGGTCAG+AACGAGGC/2 141 * 0 0 * * 0 0 ATTTTTTATTAATTTTATTTAAATATAAATTTTATTAATATATATTAATATATTTTATATATTTAAATTTTTAAAATTTTTAATATTATTTAATATTAAAATAAAAATATTTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF::FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_7_R1.fq.gz_C_to_T.fastq and zr3644_7_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:19370:1407_1:N:0:ACGGTCAG+AACGAGGC/1 83 NC_047560.1_GA_converted 3647189 0 40M2I5M1I67M = 3647192 115 TACATTTTTTATCAATTTTATCTAAATATAAATTTTATCAACATATATTAATATATTTTACATATCTAAACTCCTAAAATTTCTAATATCATTCAATACTAAAATAAAAATATCC F:FFFFFFFFFF:FFFFFFFF,FFFFF:FFFFFF:FFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFF AS:i:-25 XS:i:-37 XN:i:0 XM:i:1 XO:i:2 XG:i:3 NM:i:4 MD:Z:101C10 YS:i:-25 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:19370:1407_2:N:0:ACGGTCAG+AACGAGGC/2 163 NC_047560.1_GA_converted 3647192 0 37M2I5M1I70M = 3647189 -115 ATTTTTTATCAATTTTATCTAAATATAAATTTTATCAACATATATTAATATATTTTACATATCTAAACTCCTAAAATTTCTAATATCATTCAATACTAAAATAAAAATATCCATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFF::FFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFF:FFFF AS:i:-25 XS:i:-43 XN:i:0 XM:i:1 XO:i:2 XG:i:3 NM:i:4 MD:Z:98C13 YS:i:-25 YT:Z:CP >>> Writing bisulfite mapping results to zr3644_7_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73220 (73.22%) aligned concordantly 0 times 11929 (11.93%) aligned concordantly exactly 1 time 14851 (14.85%) aligned concordantly >1 times 26.78% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73194 (73.19%) aligned concordantly 0 times 100000 reads; of these:11972 ( 11.97100000% () aligned concordantly exactly 1 time 14834 (100.0014.83%%) were paired; of these:) aligned concordantly >1 times 26.8173442% ( overall alignment rate73.44 %) aligned concordantly 0 times 11753 (11.75%) aligned concordantly exactly 1 time 14805 (14.80%) aligned concordantly >1 times 26.56% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73214 (73.21%) aligned concordantly 0 times 11990 (11.99%) aligned concordantly exactly 1 time 14796 (14.80%) aligned concordantly >1 times 26.79% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_7_R1.fq.gz_C_to_T.fastq, zr3644_7_R1.fq.gz_G_to_A.fastq, zr3644_7_R2.fq.gz_C_to_T.fastq and zr3644_7_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60610 Mapping efficiency: 60.6% Sequence pairs with no alignments under any condition: 22770 Sequence pairs did not map uniquely: 16620 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15203 ((converted) top strand) GA/CT/CT: 15012 (complementary to (converted) top strand) GA/CT/GA: 15206 (complementary to (converted) bottom strand) CT/GA/GA: 15189 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2136064 Total methylated C's in CpG context: 28501 Total methylated C's in CHG context: 1762 Total methylated C's in CHH context: 7409 Total methylated C's in Unknown context: 65 Total unmethylated C's in CpG context: 244939 Total unmethylated C's in CHG context: 366947 Total unmethylated C's in CHH context: 1486506 Total unmethylated C's in Unknown context: 5316 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.2% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_8_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_8_R1.fq.gz Writing a C -> T converted version of the input file zr3644_8_R1.fq.gz to zr3644_8_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_8_R1.fq.gz to zr3644_8_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_8_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fq.gz Writing a C -> T converted version of the input file zr3644_8_R2.fq.gz to zr3644_8_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_8_R2.fq.gz to zr3644_8_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_8_R2.fq.gz (100001 sequences in total) Input files are zr3644_8_R1.fq.gz_C_to_T.fastq and zr3644_8_R1.fq.gz_G_to_A.fastq and zr3644_8_R2.fq.gz_C_to_T.fastq and zr3644_8_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_8_R1.fq.gz_C_to_T.fastq and zr3644_8_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2899:1000_1:N:0:NGCAAGCC+CGGATGCT/1 77 * 0 0 * * 0 0 TTAATTAAATATATTAAAATAAATTTTAAATTTAAAAATAATATTAATTATATATTATATATATTAATATTATTTTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2899:1000_2:N:0:NGCAAGCC+CGGATGCT/2 141 * 0 0 * * 0 0 ATTAATATATATAATATATAATTAATATTATTTTTAAATTTAAAATTTATTTTAATATATTTAATTAAAAATAATTAA ,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_8_R1.fq.gz_G_to_A.fastq and zr3644_8_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2899:1000_1:N:0:NGCAAGCC+CGGATGCT/1 99 NC_047564.1_GA_converted 28353577 39 78M = 28353567 -88 TTAATCAAATATACTAAAATAAACTTTAAATCTAAAAATAACATTAACTATATATCATATACATCAATATTATTTTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFF AS:i:0 XS:i:-46 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:78 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2899:1000_2:N:0:NGCAAGCC+CGGATGCT/2 147 NC_047564.1_GA_converted 28353567 39 78M = 28353577 88 TCAATTATTTTTAATCAAATATACTAAAATAAACTTTAAATCTAAAAATAACATTAACTATATATCATATACATCAAT F:FFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF, AS:i:0 XS:i:-46 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:78 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_8_R1.fq.gz_G_to_A.fastq and zr3644_8_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2899:1000_1:N:0:NGCAAGCC+CGGATGCT/1 77 * 0 0 * * 0 0 TTAATCAAATATACTAAAATAAACTTTAAATCTAAAAATAACATTAACTATATATCATATACATCAATATTATTTTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2899:1000_2:N:0:NGCAAGCC+CGGATGCT/2 141 * 0 0 * * 0 0 ATTGATGTATATGATATATAGTTAATGTTATTTTTAGATTTAAAGTTTATTTTAGTATATTTGATTAAAAATAATTGA ,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_8_R1.fq.gz_C_to_T.fastq and zr3644_8_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2899:1000_1:N:0:NGCAAGCC+CGGATGCT/1 77 * 0 0 * * 0 0 TTAATTAAATATATTAAAATAAATTTTAAATTTAAAAATAATATTAATTATATATTATATATATTAATATTATTTTTA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2899:1000_2:N:0:NGCAAGCC+CGGATGCT/2 141 * 0 0 * * 0 0 ATTAATATATATAATATATAATTAATATTATTTTTAAATTTAAAATTTATTTTAATATATTTAATTAAAAATAATTAA ,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to zr3644_8_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:23665:4272_1:N:0:GGCAAGCC+CGGATGCT NW_022994997.1 297112 100000100000 reads; of these: reads; of these: 100000100000 ( (100.00%) were paired; of these: 100.0072716% () were paired; of these:72.72 % ) aligned concordantly 0 times72891 ( 72.8912010% () aligned concordantly 0 times12.01 % ) aligned concordantly exactly 1 time11910 ( 11.9115274% () aligned concordantly exactly 1 time15.27 % ) aligned concordantly >1 times15199 (27.2815.20%% overall alignment rate) aligned concordantly >1 times 27.11% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72731 (72.73%) aligned concordantly 0 times 11825 (11.82%) aligned concordantly exactly 1 time 15444 (15.44%) aligned concordantly >1 times 27.27100000% reads; of these: overall alignment rate 100000 (100.00%) were paired; of these: 72630 (72.63%) aligned concordantly 0 times 12065 (12.06%) aligned concordantly exactly 1 time 15305 (15.30%) aligned concordantly >1 times 27.37% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_8_R1.fq.gz_C_to_T.fastq, zr3644_8_R1.fq.gz_G_to_A.fastq, zr3644_8_R2.fq.gz_C_to_T.fastq and zr3644_8_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61058 Mapping efficiency: 61.1% Sequence pairs with no alignments under any condition: 21754 Sequence pairs did not map uniquely: 17188 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15358 ((converted) top strand) GA/CT/CT: 15264 (complementary to (converted) top strand) GA/CT/GA: 15255 (complementary to (converted) bottom strand) CT/GA/GA: 15180 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2142676 Total methylated C's in CpG context: 29044 Total methylated C's in CHG context: 1764 Total methylated C's in CHH context: 8115 Total methylated C's in Unknown context: 64 Total unmethylated C's in CpG context: 247554 Total unmethylated C's in CHG context: 371803 Total unmethylated C's in CHH context: 1484396 Total unmethylated C's in Unknown context: 5274 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.2% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fq.gz Writing a C -> T converted version of the input file zr3644_9_R1.fq.gz to zr3644_9_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_9_R1.fq.gz to zr3644_9_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_9_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fq.gz Writing a C -> T converted version of the input file zr3644_9_R2.fq.gz to zr3644_9_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zr3644_9_R2.fq.gz to zr3644_9_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zr3644_9_R2.fq.gz (100001 sequences in total) Input files are zr3644_9_R1.fq.gz_C_to_T.fastq and zr3644_9_R1.fq.gz_G_to_A.fastq and zr3644_9_R2.fq.gz_C_to_T.fastq and zr3644_9_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zr3644_9_R1.fq.gz_C_to_T.fastq and zr3644_9_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1922:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATAGATAAATTAATAAGGTG FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1922:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TCTATATCTTTACCTCACAA FF:FFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zr3644_9_R1.fq.gz_G_to_A.fastq and zr3644_9_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1922:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 99 NC_047565.1_GA_converted 35597653 0 20M = 35597663 30 ATAAATAAATTAATAAAATA FFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6T13 YS:i:-12 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1922:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 147 NC_047565.1_GA_converted 35597663 0 20M = 35597653 -30 TTATAAAATAAAAATATAAA FFFFFFFFFFFFFFFFF:FF AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:1A12C5 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zr3644_9_R1.fq.gz_G_to_A.fastq and zr3644_9_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1922:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 83 NC_047561.1_CT_converted 4552158 0 20M = 4551938 -240 TATTTTATTAATTTATTTAT FFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:6T13 YS:i:-11 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1922:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 163 NC_047561.1_CT_converted 4551938 0 6M2D14M = 4552158 240 TTTATATTTTTATTTTATAA FF:FFFFFFFFFFFFFFFFF AS:i:-11 XN:i:0 XM:i:0 XO:i:1 XG:i:2 NM:i:2 MD:Z:6^TT14 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zr3644_9_R1.fq.gz_C_to_T.fastq and zr3644_9_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1922:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 83 NC_047562.1_GA_converted 28321005 42 20M = 28321020 35 CACCTTATTAATTTATCTAT FFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:20 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1922:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 163 NC_047562.1_GA_converted 28321020 42 20M = 28321005 -35 TCTATATCTTTACCTCACAA FF:FFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:20 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to zr3644_9_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72160 (72.16%) aligned concordantly 0 times 12033 (12.03%) aligned concordantly exactly 1 time 15807 (15.81%) aligned concordantly >1 times 27.84% overall alignment rate 100000 reads; of these: 100000 (100000100.00100000 reads; of these:% reads; of these: ) were paired; of these: 100000 100000 (72275 ( (72.28%) aligned concordantly 0 times 12045100.00 (%100.0012.04) were paired; of these:%% ) were paired; of these:) aligned concordantly exactly 1 time 72552 (720151568072.55 ( (%72.0215.68) aligned concordantly 0 times%% ) aligned concordantly 0 times) aligned concordantly >1 times 11928 27.73 (12145%11.93 ( overall alignment rate%12.14 ) aligned concordantly exactly 1 time% ) aligned concordantly exactly 1 time 15520 (1584015.52 (%15.84) aligned concordantly >1 times% ) aligned concordantly >1 times27.45 %27.98 overall alignment rate% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zr3644_9_R1.fq.gz_C_to_T.fastq, zr3644_9_R1.fq.gz_G_to_A.fastq, zr3644_9_R2.fq.gz_C_to_T.fastq and zr3644_9_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61092 Mapping efficiency: 61.1% Sequence pairs with no alignments under any condition: 20677 Sequence pairs did not map uniquely: 18231 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15406 ((converted) top strand) GA/CT/CT: 14990 (complementary to (converted) top strand) GA/CT/GA: 15383 (complementary to (converted) bottom strand) CT/GA/GA: 15313 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2114911 Total methylated C's in CpG context: 29822 Total methylated C's in CHG context: 1724 Total methylated C's in CHH context: 7855 Total methylated C's in Unknown context: 76 Total unmethylated C's in CpG context: 245639 Total unmethylated C's in CHG context: 368266 Total unmethylated C's in CHH context: 1461605 Total unmethylated C's in Unknown context: 5097 C methylated in CpG context: 10.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R1.fq.gz Writing a C -> T converted version of the input file zrtg3616_1_R1.fq.gz to zrtg3616_1_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_1_R1.fq.gz to zrtg3616_1_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_1_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R2.fq.gz Writing a C -> T converted version of the input file zrtg3616_1_R2.fq.gz to zrtg3616_1_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_1_R2.fq.gz to zrtg3616_1_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_1_R2.fq.gz (100001 sequences in total) Input files are zrtg3616_1_R1.fq.gz_C_to_T.fastq and zrtg3616_1_R1.fq.gz_G_to_A.fastq and zrtg3616_1_R2.fq.gz_C_to_T.fastq and zrtg3616_1_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3616_1_R1.fq.gz_C_to_T.fastq and zrtg3616_1_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:2293:1047_1:N:0:NCCGCACT+NGAGGTCG/1 77 * 0 0 * * 0 0 ATATTTTTTTATTTTATATATTTTTATATTTTTTTATTTTTTATTTTATTTTAAAATTATAAATATAAAAATTATTAAAAAAATTATAAAAAAATTTATTATTATTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP A00564:290:HLTHCDSXY:2:1101:2293:1047_2:N:0:NCCGCACT+NGAGGTCG/2 141 * 0 0 * * 0 0 TTATTATATAAATTTAATAATAATTATATATAATATATAAATATAAATAATAATAAATTTTTTTATAATTTTTTTAATAATTTTTATATTTATAATTTTAAAATAAAATAAAA FFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3616_1_R1.fq.gz_G_to_A.fastq and zrtg3616_1_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:2293:1047_1:N:0:NCCGCACT+NGAGGTCG/1 77 * 0 0 * * 0 0 ATATTTTTTTATTTTACACATCTTCATATTTTCCTATTTTTTATTTTATTTTAAAATTATAAATATAAAAATCATCAAAAAAATTATAAAAAAACTTATTACTATTTATATCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP A00564:290:HLTHCDSXY:2:1101:2293:1047_2:N:0:NCCGCACT+NGAGGTCG/2 141 * 0 0 * * 0 0 TTGTTGTATAAGTTTGATAATAATTATATGTGGTATATGGATATAAATAGTAATAAGTTTTTTTATAATTTTTTTGATGATTTTTATATTTATAATTTTAAAATAAAATAAAA FFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3616_1_R1.fq.gz_G_to_A.fastq and zrtg3616_1_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:2293:1047_1:N:0:NCCGCACT+NGAGGTCG/1 77 * 0 0 * * 0 0 ATATTTTTTTATTTTACACATCTTCATATTTTCCTATTTTTTATTTTATTTTAAAATTATAAATATAAAAATCATCAAAAAAATTATAAAAAAACTTATTACTATTTATATCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP A00564:290:HLTHCDSXY:2:1101:2293:1047_2:N:0:NCCGCACT+NGAGGTCG/2 141 * 0 0 * * 0 0 TTGTTGTATAAGTTTGATAATAATTATATGTGGTATATGGATATAAATAGTAATAAGTTTTTTTATAATTTTTTTGATGATTTTTATATTTATAATTTTAAAATAAAATAAAA FFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3616_1_R1.fq.gz_C_to_T.fastq and zrtg3616_1_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:2293:1047_1:N:0:NCCGCACT+NGAGGTCG/1 77 * 0 0 * * 0 0 ATATTTTTTTATTTTATATATTTTTATATTTTTTTATTTTTTATTTTATTTTAAAATTATAAATATAAAAATTATTAAAAAAATTATAAAAAAATTTATTATTATTTATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF: YT:Z:UP A00564:290:HLTHCDSXY:2:1101:2293:1047_2:N:0:NCCGCACT+NGAGGTCG/2 141 * 0 0 * * 0 0 TTATTATATAAATTTAATAATAATTATATATAATATATAAATATAAATAATAATAAATTTTTTTATAATTTTTTTAATAATTTTTATATTTATAATTTTAAAATAAAATAAAA FFFFFFF:FFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3616_1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 71414 (71.41%) aligned concordantly 0 times 12357 (12.36%) aligned concordantly exactly 1 time 16229 (16.23%) aligned concordantly >1 times 28.59% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71493 (71.49%) aligned concordantly 0 times 12293 (12.29%) aligned concordantly exactly 1 time 16214 (16.21%) aligned concordantly >1 times 28.51% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71512 (71.51%) aligned concordantly 0 times 12419 (12.42%) aligned concordantly exactly 1 time 16069 (16.07%) aligned concordantly >1 times 28.49% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71725 (71.72%) aligned concordantly 0 times 12123 (12.12%) aligned concordantly exactly 1 time 16152 (16.15%) aligned concordantly >1 times 28.27% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3616_1_R1.fq.gz_C_to_T.fastq, zrtg3616_1_R1.fq.gz_G_to_A.fastq, zrtg3616_1_R2.fq.gz_C_to_T.fastq and zrtg3616_1_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 62078 Mapping efficiency: 62.1% Sequence pairs with no alignments under any condition: 18843 Sequence pairs did not map uniquely: 19079 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15615 ((converted) top strand) GA/CT/CT: 15682 (complementary to (converted) top strand) GA/CT/GA: 15245 (complementary to (converted) bottom strand) CT/GA/GA: 15536 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2097641 Total methylated C's in CpG context: 31375 Total methylated C's in CHG context: 1898 Total methylated C's in CHH context: 8727 Total methylated C's in Unknown context: 90 Total unmethylated C's in CpG context: 258663 Total unmethylated C's in CHG context: 378675 Total unmethylated C's in CHH context: 1418303 Total unmethylated C's in Unknown context: 4928 C methylated in CpG context: 10.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 1.8% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R1.fq.gz Writing a C -> T converted version of the input file zrtg3616_2_R1.fq.gz to zrtg3616_2_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_2_R1.fq.gz to zrtg3616_2_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_2_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R2.fq.gz Writing a C -> T converted version of the input file zrtg3616_2_R2.fq.gz to zrtg3616_2_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_2_R2.fq.gz to zrtg3616_2_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_2_R2.fq.gz (100001 sequences in total) Input files are zrtg3616_2_R1.fq.gz_C_to_T.fastq and zrtg3616_2_R1.fq.gz_G_to_A.fastq and zrtg3616_2_R2.fq.gz_C_to_T.fastq and zrtg3616_2_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3616_2_R1.fq.gz_C_to_T.fastq and zrtg3616_2_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1461:1047_1:N:0:NCACCAGG+NTTCCATA/1 77 * 0 0 * * 0 0 AATAAAATTTTTATATGAATAATTATAAAAAAATTATGATTTTTATAAAAAAAAATATTTTAATTAATATTTTTAATAAATTAATTATAAATAAAAATTATATATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF,FFFFFFFFF:FFFFFFFFF,FFFFFF:FF:FFFFFFFFFFFFFFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1461:1047_2:N:0:NCACCAGG+NTTCCATA/2 141 * 0 0 * * 0 0 TTATTTATAATTAATTTATTAAAAATATTAATTAAAATATTTTTTTTTATAAAAATCATAATTTTTTTATAATTATTCATATAAAAATTTTATTATCATTTTTTT ::FFFFF::F::FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:FFFF,FFFFFFFFFFFFF::FFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3616_2_R1.fq.gz_G_to_A.fastq and zrtg3616_2_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1461:1047_1:N:0:NCACCAGG+NTTCCATA/1 77 * 0 0 * * 0 0 AATAAAATTTCCACACAAACAACTACAAAAAAATTACAATCCTTACAAAAAAAAATATCCCAATTAACATCTTTAATAAACCAACTACAAACAAAAATTATATACATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF,FFFFFFFFF:FFFFFFFFF,FFFFFF:FF:FFFFFFFFFFFFFFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1461:1047_2:N:0:NCACCAGG+NTTCCATA/2 141 * 0 0 * * 0 0 TTGTTTGTAGTTGGTTTATTAAAGATGTTAATTGGGATATTTTTTTTTGTAAGGATTGTAATTTTTTTGTAGTTGTTTGTGTGGAAATTTTATTGTTGTTTTTTT ::FFFFF::F::FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:FFFF,FFFFFFFFFFFFF::FFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3616_2_R1.fq.gz_G_to_A.fastq and zrtg3616_2_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1461:1047_1:N:0:NCACCAGG+NTTCCATA/1 83 NC_047563.1_CT_converted 6394288 40 32M1I75M = 6394302 118 AATGTATATAATTTTTGTTTGTAGTTGGTTTATTAAAGATGTTAATTGGGATATTTTTTTTTGTAAGGATTGTAATTTTTTTGTAGTTGTTTGTGTGGAAATTTTATT FFFFFFFFFFFFFFF:FF:FFFFFF,FFFFFFFFF:FFFFFFFFF,FFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:83T23 YS:i:-14 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1461:1047_2:N:0:NCACCAGG+NTTCCATA/2 163 NC_047563.1_CT_converted 6394302 40 18M1I86M = 6394288 -118 TTGTTTGTAGTTGGTTTATTAAAGATGTTAATTGGGATATTTTTTTTTGTAAGGATTGTAATTTTTTTGTAGTTGTTTGTGTGGAAATTTTATTGTTGTTTTTTT ::FFFFF::F::FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:FFFF,FFFFFFFFFFFFF::FFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:F AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:69T34 YS:i:-14 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3616_2_R1.fq.gz_C_to_T.fastq and zrtg3616_2_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1461:1047_1:N:0:NCACCAGG+NTTCCATA/1 77 * 0 0 * * 0 0 AATAAAATTTTTATATGAATAATTATAAAAAAATTATGATTTTTATAAAAAAAAATATTTTAATTAATATTTTTAATAAATTAATTATAAATAAAAATTATATATATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF,FFFFFFFFF:FFFFFFFFF,FFFFFF:FF:FFFFFFFFFFFFFFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1461:1047_2:N:0:NCACCAGG+NTTCCATA/2 141 * 0 0 * * 0 0 TTATTTATAATTAATTTATTAAAAATATTAATTAAAATATTTTTTTTTATAAAAATCATAATTTTTTTATAATTATTCATATAAAAATTTTATTATCATTTTTTT ::FFFFF::F::FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFFF:FFFF,FFFFFFFFFFFFF::FFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to zrtg3616_2_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 71532 (71.53%) aligned concordantly 0 times 12453 (12.45%) aligned concordantly exactly 1 time 16015 (16.02%) aligned concordantly >1 times 28.47% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71385 (71.39%) aligned concordantly 0 times 12518 (12.52%) aligned concordantly exactly 1 time 16097 (16.10%) aligned concordantly >1 times 28.61% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71789 (71.79%) aligned concordantly 0 times 12195 (12.20100000% reads; of these:) aligned concordantly exactly 1 time 10000016016 ( (16.02%) aligned concordantly >1 times 28.21% overall alignment rate 100.00%) were paired; of these: 71823 (71.82%) aligned concordantly 0 times 12140 (12.14%) aligned concordantly exactly 1 time 16037 (16.04%) aligned concordantly >1 times 28.18% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3616_2_R1.fq.gz_C_to_T.fastq, zrtg3616_2_R1.fq.gz_G_to_A.fastq, zrtg3616_2_R2.fq.gz_C_to_T.fastq and zrtg3616_2_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61847 Mapping efficiency: 61.8% Sequence pairs with no alignments under any condition: 19291 Sequence pairs did not map uniquely: 18862 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15384 ((converted) top strand) GA/CT/CT: 15310 (complementary to (converted) top strand) GA/CT/GA: 15418 (complementary to (converted) bottom strand) CT/GA/GA: 15735 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2080161 Total methylated C's in CpG context: 30602 Total methylated C's in CHG context: 1923 Total methylated C's in CHH context: 7653 Total methylated C's in Unknown context: 76 Total unmethylated C's in CpG context: 255192 Total unmethylated C's in CHG context: 374869 Total unmethylated C's in CHH context: 1409922 Total unmethylated C's in Unknown context: 4821 C methylated in CpG context: 10.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R1.fq.gz Writing a C -> T converted version of the input file zrtg3616_3_R1.fq.gz to zrtg3616_3_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_3_R1.fq.gz to zrtg3616_3_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_3_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R2.fq.gz Writing a C -> T converted version of the input file zrtg3616_3_R2.fq.gz to zrtg3616_3_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_3_R2.fq.gz to zrtg3616_3_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_3_R2.fq.gz (100001 sequences in total) Input files are zrtg3616_3_R1.fq.gz_C_to_T.fastq and zrtg3616_3_R1.fq.gz_G_to_A.fastq and zrtg3616_3_R2.fq.gz_C_to_T.fastq and zrtg3616_3_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3616_3_R1.fq.gz_C_to_T.fastq and zrtg3616_3_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1154:1047_1:N:0:NGTAACTC+NCACCAAC/1 77 * 0 0 * * 0 0 TTTTATTTTTAATAAAATATTTTAATTATTTTAAATAATTTTTTTAAAATATATTTTATATTTATAAAATTTTAAAAATTATAATTAATTAAAATATAAAATT FFFFFFFFFFFF:FF,:F:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1154:1047_2:N:0:NGTAACTC+NCACCAAC/2 141 * 0 0 * * 0 0 ATTAATTATAATTTTTAAAATTTTATAAATATAAAATATATTTTAAAAAAATTATTTAAAATAATTAAAATATTTTATTAAAAATAAAATTTTTTTATTAATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3616_3_R1.fq.gz_G_to_A.fastq and zrtg3616_3_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1154:1047_1:N:0:NGTAACTC+NCACCAAC/1 99 NC_047560.1_GA_converted 3318602 1 103M = 3318587 -118 TTCTACTTCCAATAAAACATCTCAATCATCTCAAATAACTTTTTTAAAACATATTTTATACCCACAAAATCTCAAAAACTATAATTAATCAAAACACAAAACT FFFFFFFFFFFF:FF,:F:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:103 YS:i:0 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1154:1047_2:N:0:NGTAACTC+NCACCAAC/2 147 NC_047560.1_GA_converted 3318587 1 104M = 3318602 118 AAATCAACAAAAAAATTCTACTTCCAATAAAACATCTCAATCATCTCAAATAACTTTTTTAAAACATATTTTATACCCACAAAATCTCAAAAACTATAATTAAT FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:104 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3616_3_R1.fq.gz_G_to_A.fastq and zrtg3616_3_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1154:1047_1:N:0:NGTAACTC+NCACCAAC/1 83 NC_047560.1_CT_converted 37185308 1 103M = 37185322 118 AGTTTTGTGTTTTGATTAATTATAGTTTTTGAGATTTTGTGGGTATAAAATATGTTTTAAAAAAGTTATTTGAGATGATTGAGATGTTTTATTGGAAGTAGAA FFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:F:,FF:FFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:103 YS:i:0 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1154:1047_2:N:0:NGTAACTC+NCACCAAC/2 163 NC_047560.1_CT_converted 37185322 1 104M = 37185308 -118 ATTAATTATAGTTTTTGAGATTTTGTGGGTATAAAATATGTTTTAAAAAAGTTATTTGAGATGATTGAGATGTTTTATTGGAAGTAGAATTTTTTTGTTGATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:104 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3616_3_R1.fq.gz_C_to_T.fastq and zrtg3616_3_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1154:1047_1:N:0:NGTAACTC+NCACCAAC/1 77 * 0 0 * * 0 0 TTTTATTTTTAATAAAATATTTTAATTATTTTAAATAATTTTTTTAAAATATATTTTATATTTATAAAATTTTAAAAATTATAATTAATTAAAATATAAAATT FFFFFFFFFFFF:FF,:F:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF,:FFFFFFFFFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1154:1047_2:N:0:NGTAACTC+NCACCAAC/2 141 * 0 0 * * 0 0 ATTAATTATAATTTTTAAAATTTTATAAATATAAAATATATTTTAAAAAAATTATTTAAAATAATTAAAATATTTTATTAAAAATAAAATTTTTTTATTAATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3616_3_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 71531 (71.53%) aligned concordantly 0 times 12122 (12.12%) aligned concordantly exactly 1 time 16347 (16.35%) aligned concordantly >1 times 28.47% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71223 (71.22%) aligned concordantly 0 times 12493 (12.49%) aligned concordantly exactly 1 time 16284 (16.28%) aligned concordantly >1 times 28.78% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71351 (71.35%) aligned concordantly 0 times 12448 (12.45%) aligned concordantly exactly 1 time 16201 (16.20%) aligned concordantly >1 times 28.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71230 (71.23%) aligned concordantly 0 times 12545 (12.54%) aligned concordantly exactly 1 time 16225 (16.23%) aligned concordantly >1 times 28.77% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3616_3_R1.fq.gz_C_to_T.fastq, zrtg3616_3_R1.fq.gz_G_to_A.fastq, zrtg3616_3_R2.fq.gz_C_to_T.fastq and zrtg3616_3_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61506 Mapping efficiency: 61.5% Sequence pairs with no alignments under any condition: 18728 Sequence pairs did not map uniquely: 19766 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15466 ((converted) top strand) GA/CT/CT: 15481 (complementary to (converted) top strand) GA/CT/GA: 15358 (complementary to (converted) bottom strand) CT/GA/GA: 15201 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1975265 Total methylated C's in CpG context: 29898 Total methylated C's in CHG context: 1808 Total methylated C's in CHH context: 7634 Total methylated C's in Unknown context: 63 Total unmethylated C's in CpG context: 236799 Total unmethylated C's in CHG context: 355129 Total unmethylated C's in CHH context: 1343997 Total unmethylated C's in Unknown context: 4788 C methylated in CpG context: 11.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 0h 0m 48s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R1.fq.gz Writing a C -> T converted version of the input file zrtg3616_4_R1.fq.gz to zrtg3616_4_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_4_R1.fq.gz to zrtg3616_4_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_4_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R2.fq.gz Writing a C -> T converted version of the input file zrtg3616_4_R2.fq.gz to zrtg3616_4_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_4_R2.fq.gz to zrtg3616_4_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_4_R2.fq.gz (100001 sequences in total) Input files are zrtg3616_4_R1.fq.gz_C_to_T.fastq and zrtg3616_4_R1.fq.gz_G_to_A.fastq and zrtg3616_4_R2.fq.gz_C_to_T.fastq and zrtg3616_4_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3616_4_R1.fq.gz_C_to_T.fastq and zrtg3616_4_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1063:1047_1:N:0:NCCGGCCG+NATATTGC/1 77 * 0 0 * * 0 0 TATAAATATTTTATTTTATAATATATTATTTTAATTTTTTAATTAATATTTATATTTATATTTTAAAAATATTTTAATAAATTTTATATATATATTTATTAATTATTTAAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF::FFFFFFFFFFFFFF:F,FF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1063:1047_2:N:0:NCCGGCCG+NATATTGC/2 141 * 0 0 * * 0 0 TTAATAAATATATATATAAAATTTATTAAAATATTTTTAAAATATAAATATAAATATTAATTAAAAAATTAAAATAATATATTATAAAATAAAATATTTATATTATTAAAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3616_4_R1.fq.gz_G_to_A.fastq and zrtg3616_4_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1063:1047_1:N:0:NCCGGCCG+NATATTGC/1 99 NC_047566.1_GA_converted 25733567 1 114M = 25733555 -126 TACAAATATTTTATCTTACAATACATTATCCTAACCTTTCAATTAACATTTACATTCATATTTTAAAAATATCTCAATAAATTTTACATATATATCTACCAACTACTCAAAACT FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF::FFFFFFFFFFFFFF:F,FF AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:35T9T6A61 YS:i:-18 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1063:1047_2:N:0:NCCGGCCG+NATATTGC/2 147 NC_047566.1_GA_converted 25733555 1 114M = 25733567 126 ATATCTCAATAATACAAATATTTTATCTTACAATACATTATCCTAACCTTTCAATTAACATTTACATTCATATTTTAAAAATATCTCAATAAATTTTACATATATATCTACCAA F:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:47T9T6A49 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3616_4_R1.fq.gz_G_to_A.fastq and zrtg3616_4_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1063:1047_1:N:0:NCCGGCCG+NATATTGC/1 83 NC_047566.1_CT_converted 57109930 6 114M = 57109942 126 AGTTTTGAGTAGTTGGTAGATATATATGTAAAATTTATTGAGATATTTTTAAAATATGAATGTAAATGTTAATTGAAAGGTTAGGATAATGTATTGTAAGATAAAATATTTGTA FF,F:FFFFFFFFFFFFFF::FFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:61T6A9A35 YS:i:-18 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1063:1047_2:N:0:NCCGGCCG+NATATTGC/2 163 NC_047566.1_CT_converted 57109942 6 114M = 57109930 -126 TTGGTAGATATATATGTAAAATTTATTGAGATATTTTTAAAATATGAATGTAAATGTTAATTGAAAGGTTAGGATAATGTATTGTAAGATAAAATATTTGTATTATTGAGATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:49T6A9A47 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3616_4_R1.fq.gz_C_to_T.fastq and zrtg3616_4_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1063:1047_1:N:0:NCCGGCCG+NATATTGC/1 77 * 0 0 * * 0 0 TATAAATATTTTATTTTATAATATATTATTTTAATTTTTTAATTAATATTTATATTTATATTTTAAAAATATTTTAATAAATTTTATATATATATTTATTAATTATTTAAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFF,FF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF::FFFFFFFFFFFFFF:F,FF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1063:1047_2:N:0:NCCGGCCG+NATATTGC/2 141 * 0 0 * * 0 0 TTAATAAATATATATATAAAATTTATTAAAATATTTTTAAAATATAAATATAAATATTAATTAAAAAATTAAAATAATATATTATAAAATAAAATATTTATATTATTAAAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F YT:Z:UP >>> Writing bisulfite mapping results to zrtg3616_4_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 71505 (71.50%) aligned concordantly 0 times 12180 (12.18%) aligned concordantly exactly 1 time 16315100000 ( reads; of these:16.32 % ) aligned concordantly >1 times100000 (28.50% overall alignment rate 100.00%) were paired; of these: 71404 (71.40%) aligned concordantly 0 times 12322 (12.32%) aligned concordantly exactly 1 time 16274 (16.27%) aligned concordantly >1 times 28.60% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71305 (71.31%) aligned concordantly 0 times 12474 (12.47%) aligned concordantly exactly 1 time 16221 (16.22%) aligned concordantly >1 times 28.70% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71551 (71.55%) aligned concordantly 0 times 12330 (12.33%) aligned concordantly exactly 1 time 16119 (16.12%) aligned concordantly >1 times 28.45% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3616_4_R1.fq.gz_C_to_T.fastq, zrtg3616_4_R1.fq.gz_G_to_A.fastq, zrtg3616_4_R2.fq.gz_C_to_T.fastq and zrtg3616_4_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61653 Mapping efficiency: 61.7% Sequence pairs with no alignments under any condition: 18849 Sequence pairs did not map uniquely: 19498 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15417 ((converted) top strand) GA/CT/CT: 15210 (complementary to (converted) top strand) GA/CT/GA: 15469 (complementary to (converted) bottom strand) CT/GA/GA: 15557 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2033622 Total methylated C's in CpG context: 29878 Total methylated C's in CHG context: 1920 Total methylated C's in CHH context: 7954 Total methylated C's in Unknown context: 72 Total unmethylated C's in CpG context: 247745 Total unmethylated C's in CHG context: 368893 Total unmethylated C's in CHH context: 1377232 Total unmethylated C's in Unknown context: 4794 C methylated in CpG context: 10.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R1.fq.gz Writing a C -> T converted version of the input file zrtg3616_5_R1.fq.gz to zrtg3616_5_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_5_R1.fq.gz to zrtg3616_5_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_5_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R2.fq.gz Writing a C -> T converted version of the input file zrtg3616_5_R2.fq.gz to zrtg3616_5_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_5_R2.fq.gz to zrtg3616_5_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_5_R2.fq.gz (100001 sequences in total) Input files are zrtg3616_5_R1.fq.gz_C_to_T.fastq and zrtg3616_5_R1.fq.gz_G_to_A.fastq and zrtg3616_5_R2.fq.gz_C_to_T.fastq and zrtg3616_5_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3616_5_R1.fq.gz_C_to_T.fastq and zrtg3616_5_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1262:1047_1:N:0:NGTAATCG+NGCGGTGA/1 77 * 0 0 * * 0 0 TGGATGGGTTTTTTTGGGTGGGTGAGTTTGTTGTAGGATATTTTGGTAGTGTAAATTGTTGGTTTTGAAGAGGATTTTAGTTGGGTTTTTGATATTGGATTTTGGATGGTGAT FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFF::FFFFFFF,FF:FFFFFFFFFFFFFFF,,FF:FFFFFFF,:FFFFFF:FFFFFFFFFFFFFFFFF: YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1262:1047_2:N:0:NGTAATCG+NGCGGTGA/2 141 * 0 0 * * 0 0 AACCCATCCTCAACAAAAAACTCTCCTATAAACAATCCCACCAAAAAAACAACTCCATCTCCACCACCTATATCACCATCCAAAATCCAATATCAAAAACCCAACTAAATTCC FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3616_5_R1.fq.gz_G_to_A.fastq and zrtg3616_5_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1262:1047_1:N:0:NGTAATCG+NGCGGTGA/1 77 * 0 0 * * 0 0 TAAATAAATTTTTTTAAATAAATAAATTTATTATAAAATATTTTAATAATATAAATTATTAATTTTAAAAAAAACTTTAATTAAATTTTTAATATTAAATTTTAAATAATAAT FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFF::FFFFFFF,FF:FFFFFFFFFFFFFFF,,FF:FFFFFFF,:FFFFFF:FFFFFFFFFFFFFFFFF: YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1262:1047_2:N:0:NGTAATCG+NGCGGTGA/2 141 * 0 0 * * 0 0 AATTTATTTTTAATAAAAAATTTTTTTATAAATAATTTTATTAAAAAAATAATTTTATTTTTATTATTTATATTATTATTTAAAATTTAATATTAAAAATTTAATTAAATTTT FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3616_5_R1.fq.gz_G_to_A.fastq and zrtg3616_5_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1262:1047_1:N:0:NGTAATCG+NGCGGTGA/1 77 * 0 0 * * 0 0 TAAATAAATTTTTTTAAATAAATAAATTTATTATAAAATATTTTAATAATATAAATTATTAATTTTAAAAAAAACTTTAATTAAATTTTTAATATTAAATTTTAAATAATAAT FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFF::FFFFFFF,FF:FFFFFFFFFFFFFFF,,FF:FFFFFFF,:FFFFFF:FFFFFFFFFFFFFFFFF: YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1262:1047_2:N:0:NGTAATCG+NGCGGTGA/2 141 * 0 0 * * 0 0 AATTTATTTTTAATAAAAAATTTTTTTATAAATAATTTTATTAAAAAAATAATTTTATTTTTATTATTTATATTATTATTTAAAATTTAATATTAAAAATTTAATTAAATTTT FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3616_5_R1.fq.gz_C_to_T.fastq and zrtg3616_5_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1262:1047_1:N:0:NGTAATCG+NGCGGTGA/1 83 NW_022994794.1_GA_converted 286564 7 113M = 286493 -184 ATCACCATCCAAAATCCAATATCAAAAACCCAACTAAAATCCTCTTCAAAACCAACAATTTACACTACCAAAATATCCTACAACAAACTCACCCACCCAAAAAAACCCATCCA :FFFFFFFFFFFFFFFFF:FFFFFF:,FFFFFFF:FF,,FFFFFFFFFFFFFFF:FF,FFFFFFF::FFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF AS:i:-18 XS:i:-24 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:27C4T5T74 YS:i:-12 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1262:1047_2:N:0:NGTAATCG+NGCGGTGA/2 163 NW_022994794.1_GA_converted 286493 7 113M = 286564 184 AACCCATCCTCAACAAAAAACTCTCCTATAAACAATCCCACCAAAAAAACAACTCCATCTCCACCACCTATATCACCATCCAAAATCCAATATCAAAAACCCAACTAAATTCC FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:F:,FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,:FFFF AS:i:-12 XS:i:-24 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:98C4T9 YS:i:-18 YT:Z:CP >>> Writing bisulfite mapping results to zrtg3616_5_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R2.fq.gz Chromosomal sequence could not be extracted for A00564:290:HLTHCDSXY:2:1101:31675:7153_1:N:0:TGTAATCG+CGCGGTGA NW_022994966.1 1 100000 reads; of these: 100000 (100.00%) were paired; of these: 71472 (71.47%) aligned concordantly 0 times 12190 (12.19%) aligned concordantly exactly 1 time 16338 (10000016.34 reads; of these:% ) aligned concordantly >1 times 10000028.53 (% overall alignment rate 100.00%) were paired; of these: 71331 (71.33%) aligned concordantly 0 times 12394 (12.39%) aligned concordantly exactly 1 time 16275 (16.27%) aligned concordantly >1 times 28.67% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71358 (71.36%) aligned concordantly 0 times 12315 (12.31%) aligned concordantly exactly 1 time 16327 (16.33%) aligned concordantly >1 times 28.64% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71157 (71.16%) aligned concordantly 0 times 12538 (12.54%) aligned concordantly exactly 1 time 16305 (16.30%) aligned concordantly >1 times 28.84% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3616_5_R1.fq.gz_C_to_T.fastq, zrtg3616_5_R1.fq.gz_G_to_A.fastq, zrtg3616_5_R2.fq.gz_C_to_T.fastq and zrtg3616_5_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61682 Mapping efficiency: 61.7% Sequence pairs with no alignments under any condition: 18693 Sequence pairs did not map uniquely: 19625 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15603 ((converted) top strand) GA/CT/CT: 15314 (complementary to (converted) top strand) GA/CT/GA: 15482 (complementary to (converted) bottom strand) CT/GA/GA: 15282 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2012509 Total methylated C's in CpG context: 28226 Total methylated C's in CHG context: 1768 Total methylated C's in CHH context: 7979 Total methylated C's in Unknown context: 76 Total unmethylated C's in CpG context: 245141 Total unmethylated C's in CHG context: 362340 Total unmethylated C's in CHH context: 1367055 Total unmethylated C's in Unknown context: 4713 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R1.fq.gz Writing a C -> T converted version of the input file zrtg3616_6_R1.fq.gz to zrtg3616_6_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_6_R1.fq.gz to zrtg3616_6_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_6_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R2.fq.gz Writing a C -> T converted version of the input file zrtg3616_6_R2.fq.gz to zrtg3616_6_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_6_R2.fq.gz to zrtg3616_6_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_6_R2.fq.gz (100001 sequences in total) Input files are zrtg3616_6_R1.fq.gz_C_to_T.fastq and zrtg3616_6_R1.fq.gz_G_to_A.fastq and zrtg3616_6_R2.fq.gz_C_to_T.fastq and zrtg3616_6_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3616_6_R1.fq.gz_C_to_T.fastq and zrtg3616_6_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1027:1047_1:N:0:NTGCAGAC+NCGGATGG/1 99 NC_047563.1_CT_converted 9720495 42 90M = 9720481 -104 TATGGAAAAAGTTTTTTTTTATAGTTATATATTAATTGAAAAGTTTTGTAAATATTGATTATTGTTGATATAGATAAAAGTTGGATTTTT FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:90 YS:i:0 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1027:1047_2:N:0:NTGCAGAC+NCGGATGG/2 147 NC_047563.1_CT_converted 9720481 42 90M = 9720495 104 GGTTGATTGATATTTATGGAAAAAGTTTTTTTTTATAGTTATATATTAATTGAAAAGTTTTGTAAATATTGATTATTGTTGATATAGATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:90 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3616_6_R1.fq.gz_G_to_A.fastq and zrtg3616_6_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1027:1047_1:N:0:NTGCAGAC+NCGGATGG/1 77 * 0 0 * * 0 0 TATAAAAAAAATTTTTTTTTATAATTATATATTAATTAAAAAATTTTATAAATATTAATTATTATTAATATAAATAAAAATTAAATTTTT FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1027:1047_2:N:0:NTGCAGAC+NCGGATGG/2 141 * 0 0 * * 0 0 TATTTATATTAATAATAATTAATATTTATAAAATTTTTTAATTAATATATAATTATAAAAAAAAATTTTTTTTATAAATATTAATTAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3616_6_R1.fq.gz_G_to_A.fastq and zrtg3616_6_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1027:1047_1:N:0:NTGCAGAC+NCGGATGG/1 77 * 0 0 * * 0 0 TATAAAAAAAATTTTTTTTTATAATTATATATTAATTAAAAAATTTTATAAATATTAATTATTATTAATATAAATAAAAATTAAATTTTT FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1027:1047_2:N:0:NTGCAGAC+NCGGATGG/2 141 * 0 0 * * 0 0 TATTTATATTAATAATAATTAATATTTATAAAATTTTTTAATTAATATATAATTATAAAAAAAAATTTTTTTTATAAATATTAATTAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3616_6_R1.fq.gz_C_to_T.fastq and zrtg3616_6_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1027:1047_1:N:0:NTGCAGAC+NCGGATGG/1 77 * 0 0 * * 0 0 TATGGAAAAAGTTTTTTTTTATAGTTATATATTAATTGAAAAGTTTTGTAAATATTGATTATTGTTGATATAGATAAAAGTTGGATTTTT FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1027:1047_2:N:0:NTGCAGAC+NCGGATGG/2 141 * 0 0 * * 0 0 TATCTATATCAACAATAATCAATATTTACAAAACTTTTCAATTAATATATAACTATAAAAAAAAACTTTTTCCATAAATATCAATCAACC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3616_6_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 71042 (71.04%) aligned concordantly 0 times 12211 (12.21%) aligned concordantly exactly 1 time 16747 (16.75%) aligned concordantly >1 times 28.96% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 70838 (70.84%) aligned concordantly 0 times 12469 (12.47%) aligned concordantly exactly 1 time 16693 (16.69%) aligned concordantly >1 times 29.16% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71339 (71.34%) aligned concordantly 0 times 12434 (12.43%) aligned concordantly exactly 1 time 16227 (16.23%) aligned concordantly >1 times 28.66% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71531 (71.53%) aligned concordantly 0 times 12170 (12.17%) aligned concordantly exactly 1 time 16299 (16.30%) aligned concordantly >1 times 28.47% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3616_6_R1.fq.gz_C_to_T.fastq, zrtg3616_6_R1.fq.gz_G_to_A.fastq, zrtg3616_6_R2.fq.gz_C_to_T.fastq and zrtg3616_6_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61511 Mapping efficiency: 61.5% Sequence pairs with no alignments under any condition: 18449 Sequence pairs did not map uniquely: 20040 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15399 ((converted) top strand) GA/CT/CT: 15229 (complementary to (converted) top strand) GA/CT/GA: 15379 (complementary to (converted) bottom strand) CT/GA/GA: 15504 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1971949 Total methylated C's in CpG context: 28429 Total methylated C's in CHG context: 1717 Total methylated C's in CHH context: 7390 Total methylated C's in Unknown context: 66 Total unmethylated C's in CpG context: 240998 Total unmethylated C's in CHG context: 356005 Total unmethylated C's in CHH context: 1337410 Total unmethylated C's in Unknown context: 4474 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R1.fq.gz Writing a C -> T converted version of the input file zrtg3616_7_R1.fq.gz to zrtg3616_7_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_7_R1.fq.gz to zrtg3616_7_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_7_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R2.fq.gz Writing a C -> T converted version of the input file zrtg3616_7_R2.fq.gz to zrtg3616_7_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_7_R2.fq.gz to zrtg3616_7_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_7_R2.fq.gz (100001 sequences in total) Input files are zrtg3616_7_R1.fq.gz_C_to_T.fastq and zrtg3616_7_R1.fq.gz_G_to_A.fastq and zrtg3616_7_R2.fq.gz_C_to_T.fastq and zrtg3616_7_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3616_7_R1.fq.gz_C_to_T.fastq and zrtg3616_7_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1624:1047_1:N:0:NAATCGGC+NTCCTACA/1 77 * 0 0 * * 0 0 TTTAATATTATTTATTTTATTATTATTTTATATAAAATATTATTTATTATATTTTATTTATATAT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1624:1047_2:N:0:NAATCGGC+NTCCTACA/2 141 * 0 0 * * 0 0 ATAATAAATAATATTTTATATAAAATAATAATAAAATAAATAATATTAAATATAAATAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3616_7_R1.fq.gz_G_to_A.fastq and zrtg3616_7_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1624:1047_1:N:0:NAATCGGC+NTCCTACA/1 77 * 0 0 * * 0 0 TCCAACACTATTTATCTCACTATTACTCTATACAAAACATTATCCATCACACTTTATCTATACAT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1624:1047_2:N:0:NAATCGGC+NTCCTACA/2 141 * 0 0 * * 0 0 GTGATGGATAATGTTTTGTATAGAGTAATAGTGAGATAAATAGTGTTGGATATAGATAGAGTGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3616_7_R1.fq.gz_G_to_A.fastq and zrtg3616_7_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1624:1047_1:N:0:NAATCGGC+NTCCTACA/1 77 * 0 0 * * 0 0 TCCAACACTATTTATCTCACTATTACTCTATACAAAACATTATCCATCACACTTTATCTATACAT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1624:1047_2:N:0:NAATCGGC+NTCCTACA/2 141 * 0 0 * * 0 0 GTGATGGATAATGTTTTGTATAGAGTAATAGTGAGATAAATAGTGTTGGATATAGATAGAGTGAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3616_7_R1.fq.gz_C_to_T.fastq and zrtg3616_7_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1624:1047_1:N:0:NAATCGGC+NTCCTACA/1 77 * 0 0 * * 0 0 TTTAATATTATTTATTTTATTATTATTTTATATAAAATATTATTTATTATATTTTATTTATATAT FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1624:1047_2:N:0:NAATCGGC+NTCCTACA/2 141 * 0 0 * * 0 0 ATAATAAATAATATTTTATATAAAATAATAATAAAATAAATAATATTAAATATAAATAAAATAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3616_7_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R2.fq.gz Chromosomal sequence could not be extracted for A00564:290:HLTHCDSXY:2:1101:26946:11334_1:N:0:CAATCGGC+TTCCTACA NC_001276.1 18122 100000 reads; of these: 100000 (100.00%) were paired; of these: 72200 (72.20%) aligned concordantly 0 times 12235 (12.23%) aligned concordantly exactly 1 time 15565 (15.56%) aligned concordantly >1 times 27.80% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71384 (71.38%) aligned concordantly 0 times 12416 (12.42%) aligned concordantly exactly 1 time 16200 (16.20%) aligned concordantly >1 times 28.62% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71458 (71.46%) aligned concordantly 0 times 12439 (12.44%) aligned concordantly exactly 1 time 16103 (16.10%) aligned concordantly >1 times 28.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71983 (71.98%) aligned concordantly 0 times 12328 (12.33%) aligned concordantly exactly 1 time 15689 (15.69%) aligned concordantly >1 times 28.02% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3616_7_R1.fq.gz_C_to_T.fastq, zrtg3616_7_R1.fq.gz_G_to_A.fastq, zrtg3616_7_R2.fq.gz_C_to_T.fastq and zrtg3616_7_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61555 Mapping efficiency: 61.6% Sequence pairs with no alignments under any condition: 19307 Sequence pairs did not map uniquely: 19138 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15617 ((converted) top strand) GA/CT/CT: 15277 (complementary to (converted) top strand) GA/CT/GA: 15198 (complementary to (converted) bottom strand) CT/GA/GA: 15462 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 1998027 Total methylated C's in CpG context: 30581 Total methylated C's in CHG context: 1797 Total methylated C's in CHH context: 7852 Total methylated C's in Unknown context: 80 Total unmethylated C's in CpG context: 239023 Total unmethylated C's in CHG context: 357714 Total unmethylated C's in CHH context: 1361060 Total unmethylated C's in Unknown context: 4895 C methylated in CpG context: 11.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R1.fq.gz Writing a C -> T converted version of the input file zrtg3616_8_R1.fq.gz to zrtg3616_8_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_8_R1.fq.gz to zrtg3616_8_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_8_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R2.fq.gz Writing a C -> T converted version of the input file zrtg3616_8_R2.fq.gz to zrtg3616_8_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3616_8_R2.fq.gz to zrtg3616_8_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3616_8_R2.fq.gz (100001 sequences in total) Input files are zrtg3616_8_R1.fq.gz_C_to_T.fastq and zrtg3616_8_R1.fq.gz_G_to_A.fastq and zrtg3616_8_R2.fq.gz_C_to_T.fastq and zrtg3616_8_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3616_8_R1.fq.gz_C_to_T.fastq and zrtg3616_8_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1172:1047_1:N:0:NATGTAGT+NATTAGTG/1 77 * 0 0 * * 0 0 TTTTATATTATTTATTTTTTTTTATATTATTTTTAATTTATTATTTATATTATTTTATATTTTATTAATATTAATTTAAATAATTTATATATTTTAATTTATAATTTTT FFFF:F:FFF:FFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF,,FFFFF,:FFFFFFFFF,:FFFFF:FF::,FFFFFFFFF:FF,,FFFF:FF:::,F::FFF:,FFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1172:1047_2:N:0:NATGTAGT+NATTAGTG/2 141 * 0 0 * * 0 0 AATATATAAAAAATATTAAATTTAATAAATTTTTTAAATAATAAAAAATTAATAATAAATATTATATAAATAAATTTTAATAAATAATTAATAAAATATATAAATAAAATTAT ,F,FFF:FFFFF:FFFFFFFFFFFFFFFFFFF:F:FFFFFFF:FF,FFFFFFFFFF:FFFF:FF:,F:FFFFF,FFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3616_8_R1.fq.gz_G_to_A.fastq and zrtg3616_8_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1172:1047_1:N:0:NATGTAGT+NATTAGTG/1 99 NW_022994850.1_GA_converted 613657 6 109M = 613766 222 TTCCATACTATTCATTTCTTCCTACACCACCTTCAATTTACTATCCACATTATCCTACATTTTACTAATATTAACCTAAATAACTTATATATTCTAATCCATAATTTCT FFFF:F:FFF:FFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF,,FFFFF,:FFFFFFFFF,:FFFFF:FF::,FFFFFFFFF:FF,,FFFF:FF:::,F::FFF:,FFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:103C5 YS:i:-6 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1172:1047_2:N:0:NATGTAGT+NATTAGTG/2 147 NW_022994850.1_GA_converted 613766 6 113M = 613657 -222 ATAATTTTATTCATACACTTCATCAACTACTCATTAAAACCTACTTATACAATATTCACTATTAATTCCTCATTATCTAAAAAATCTACTAAATCTAACATTCCCCATACATT F:FFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF,FFFFF:F,:FF:FFFF:FFFFFFFFFF,FF:FFFFFFF:F:FFFFFFFFFFFFFFFFFFF:FFFFF:FFF,F, AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:92T20 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3616_8_R1.fq.gz_G_to_A.fastq and zrtg3616_8_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1172:1047_1:N:0:NATGTAGT+NATTAGTG/1 83 NC_047559.1_CT_converted 53315383 1 109M = 53315270 -222 AGAAATTATGGATTAGAATATATAAGTTATTTAGGTTAATATTAGTAAAATGTAGGATAATGTGGATAGTAAATTGAAGGTGGTGTAGGAAGAAATGAATAGTATGGAA FFF,:FFF::F,:::FF:FFFF,,FF:FFFFFFFFF,::FF:FFFFF:,FFFFFFFFF:,FFFFF,,FFFFFFFFFF:FFFFFFFFFFFF:FFFFFFF:FFF:F:FFFF AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:5G103 YS:i:-6 YT:Z:CP A00564:290:HLTHCDSXY:2:1101:1172:1047_2:N:0:NATGTAGT+NATTAGTG/2 163 NC_047559.1_CT_converted 53315270 1 113M = 53315383 222 AATGTATGGGGAATGTTAGATTTAGTAGATTTTTTAGATAATGAGGAATTAATAGTGAATATTGTATAAGTAGGTTTTAATGAGTAGTTGATGAAGTGTATGAATAAAATTAT ,F,FFF:FFFFF:FFFFFFFFFFFFFFFFFFF:F:FFFFFFF:FF,FFFFFFFFFF:FFFF:FF:,F:FFFFF,FFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:F AS:i:-6 XS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:20A92 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3616_8_R1.fq.gz_C_to_T.fastq and zrtg3616_8_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00564:290:HLTHCDSXY:2:1101:1172:1047_1:N:0:NATGTAGT+NATTAGTG/1 77 * 0 0 * * 0 0 TTTTATATTATTTATTTTTTTTTATATTATTTTTAATTTATTATTTATATTATTTTATATTTTATTAATATTAATTTAAATAATTTATATATTTTAATTTATAATTTTT FFFF:F:FFF:FFFFFFF:FFFFFFFFFFFF:FFFFFFFFFF,,FFFFF,:FFFFFFFFF,:FFFFF:FF::,FFFFFFFFF:FF,,FFFF:FF:::,F::FFF:,FFF YT:Z:UP A00564:290:HLTHCDSXY:2:1101:1172:1047_2:N:0:NATGTAGT+NATTAGTG/2 141 * 0 0 * * 0 0 AATATATAAAAAATATTAAATTTAATAAATTTTTTAAATAATAAAAAATTAATAATAAATATTATATAAATAAATTTTAATAAATAATTAATAAAATATATAAATAAAATTAT ,F,FFF:FFFFF:FFFFFFFFFFFFFFFFFFF:F:FFFFFFF:FF,FFFFFFFFFF:FFFF:FF:,F:FFFFF,FFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFF:F YT:Z:UP >>> Writing bisulfite mapping results to zrtg3616_8_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 71616 (71.62%) aligned concordantly 0 times 12374 (12.37%) aligned concordantly exactly 1 time 16010 (16.01%) aligned concordantly >1 times 28.38% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 71261 (71.26%) aligned concordantly 0 times 12423 (12.42%) aligned concordantly exactly 1 time 16316 (16.32%) aligned concordantly >1 times 28.74% overall alignment rate 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (71528 (71.53%) aligned concordantly 0 times 12290 (12.29%) aligned concordantly exactly 1 time100.00 % ) were paired; of these:16182 ( 16.1871365% () aligned concordantly >1 times71.36 %28.47) aligned concordantly 0 times% overall alignment rate 12366 (12.37%) aligned concordantly exactly 1 time 16269 (16.27%) aligned concordantly >1 times 28.64% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3616_8_R1.fq.gz_C_to_T.fastq, zrtg3616_8_R1.fq.gz_G_to_A.fastq, zrtg3616_8_R2.fq.gz_C_to_T.fastq and zrtg3616_8_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61458 Mapping efficiency: 61.5% Sequence pairs with no alignments under any condition: 18881 Sequence pairs did not map uniquely: 19661 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15324 ((converted) top strand) GA/CT/CT: 15381 (complementary to (converted) top strand) GA/CT/GA: 15359 (complementary to (converted) bottom strand) CT/GA/GA: 15394 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2027999 Total methylated C's in CpG context: 30597 Total methylated C's in CHG context: 1889 Total methylated C's in CHH context: 8508 Total methylated C's in Unknown context: 101 Total unmethylated C's in CpG context: 247291 Total unmethylated C's in CHG context: 367521 Total unmethylated C's in CHH context: 1372193 Total unmethylated C's in Unknown context: 4708 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% C methylated in unknown context (CN or CHN): 2.1% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_10_R1.fq.gz to zrtg3644_10_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_10_R1.fq.gz to zrtg3644_10_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_10_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_10_R2.fq.gz to zrtg3644_10_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_10_R2.fq.gz to zrtg3644_10_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_10_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_10_R1.fq.gz_C_to_T.fastq and zrtg3644_10_R1.fq.gz_G_to_A.fastq and zrtg3644_10_R2.fq.gz_C_to_T.fastq and zrtg3644_10_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_10_R1.fq.gz_C_to_T.fastq and zrtg3644_10_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5412:1000_1:N:0:NCCGTTAC+TCGCTATG/1 77 * 0 0 * * 0 0 AATAAAATTTAAATTATTTATTAAATAATATTATTATATTATATTTATTAAAAATTTATAAAAAAATAAAAAAAATTAAAAAAATTTTTAATAATATTATAATAAATTAAATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFF:FFF,F:FFFFFFFF:FFFFFFFFFF:FFFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5412:1000_2:N:0:NCCGTTAC+TCGCTATG/2 141 * 0 0 * * 0 0 TTTTTATATATATTTTATATATAAATTTTTTATATATAATTTAAATTAATAAATATATATTATTAATTAAATTATTAAATTATATATTATAAATTTAATTTATTATAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF,F:FF:FFFFF:F:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_10_R1.fq.gz_G_to_A.fastq and zrtg3644_10_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5412:1000_1:N:0:NCCGTTAC+TCGCTATG/1 99 NC_047567.1_GA_converted 10679673 40 114M = 10679762 204 AATAAAACTCAAATTATTCACTAAATAACACCACCACATCACATCTACCAAAAATTTATAAAAAAACAAAAAAAACCAAAAAAATCTTTAATAATACCACAACAAATCAAATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFF:FFF,F:FFFFFFFF:FFFFFFFFFF:FFFF,F AS:i:-12 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:9T73C30 YS:i:-24 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:5412:1000_2:N:0:NCCGTTAC+TCGCTATG/2 147 NC_047567.1_GA_converted 10679762 40 115M = 10679673 -204 AATAATACCACAACAAATCAAATTTATAACATATAATTTAATAATTCAACCAATAACACATATTTACTAATTTAAATCACACATAAAAAACTTACATATAAAACATATATAAAAA FFFFF:F:FFFFF:FF:F,FF:FFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:66T6T17A13A9 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_10_R1.fq.gz_G_to_A.fastq and zrtg3644_10_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5412:1000_1:N:0:NCCGTTAC+TCGCTATG/1 77 * 0 0 * * 0 0 AATAAAACTCAAATTATTCACTAAATAACACCACCACATCACATCTACCAAAAATTTATAAAAAAACAAAAAAAACCAAAAAAATCTTTAATAATACCACAACAAATCAAATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFF:FFF,F:FFFFFFFF:FFFFFFFFFF:FFFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5412:1000_2:N:0:NCCGTTAC+TCGCTATG/2 141 * 0 0 * * 0 0 TTTTTATATATGTTTTATATGTAAGTTTTTTATGTGTGATTTAAATTAGTAAATATGTGTTATTGGTTGAATTATTAAATTATATGTTATAAATTTGATTTGTTGTGGTATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF,F:FF:FFFFF:F:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_10_R1.fq.gz_C_to_T.fastq and zrtg3644_10_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5412:1000_1:N:0:NCCGTTAC+TCGCTATG/1 77 * 0 0 * * 0 0 AATAAAATTTAAATTATTTATTAAATAATATTATTATATTATATTTATTAAAAATTTATAAAAAAATAAAAAAAATTAAAAAAATTTTTAATAATATTATAATAAATTAAATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFF:FFF,F:FFFFFFFF:FFFFFFFFFF:FFFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5412:1000_2:N:0:NCCGTTAC+TCGCTATG/2 141 * 0 0 * * 0 0 TTTTTATATATATTTTATATATAAATTTTTTATATATAATTTAAATTAATAAATATATATTATTAATTAAATTATTAAATTATATATTATAAATTTAATTTATTATAATATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFF:FF,F:FF:FFFFF:F:FFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_10_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:6352:13150_1:N:0:ACCGTTAC+TCGCTATG NW_022994911.1 1 100000 reads; of these: 100000 (100.00%) were paired; of these: 73281 (73.28%) aligned concordantly 0 times 11869 (11.87%) aligned concordantly exactly 1 time 14850 (14.85%) aligned concordantly >1 times 26.72% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73336 (73.34%) aligned concordantly 0 times 11987 (11.99%) aligned concordantly exactly 1 time 14677 (14.68%) aligned concordantly >1 times 26.66% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73275 (73.28%) aligned concordantly 0 times 12018 (12.02%) aligned concordantly exactly 1 time 14707 (14.71%) aligned concordantly >1 times 26.73% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73121 (73.12%) aligned concordantly 0 times 12042 (12.04%) aligned concordantly exactly 1 time 14837 (14.84%) aligned concordantly >1 times 26.88% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_10_R1.fq.gz_C_to_T.fastq, zrtg3644_10_R1.fq.gz_G_to_A.fastq, zrtg3644_10_R2.fq.gz_C_to_T.fastq and zrtg3644_10_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60927 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 22647 Sequence pairs did not map uniquely: 16426 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15178 ((converted) top strand) GA/CT/CT: 15142 (complementary to (converted) top strand) GA/CT/GA: 15261 (complementary to (converted) bottom strand) CT/GA/GA: 15345 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2156193 Total methylated C's in CpG context: 29771 Total methylated C's in CHG context: 1786 Total methylated C's in CHH context: 7551 Total methylated C's in Unknown context: 68 Total unmethylated C's in CpG context: 252863 Total unmethylated C's in CHG context: 376521 Total unmethylated C's in CHH context: 1487701 Total unmethylated C's in Unknown context: 5259 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_11_R1.fq.gz to zrtg3644_11_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_11_R1.fq.gz to zrtg3644_11_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_11_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_11_R2.fq.gz to zrtg3644_11_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_11_R2.fq.gz to zrtg3644_11_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_11_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_11_R1.fq.gz_C_to_T.fastq and zrtg3644_11_R1.fq.gz_G_to_A.fastq and zrtg3644_11_R2.fq.gz_C_to_T.fastq and zrtg3644_11_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_11_R1.fq.gz_C_to_T.fastq and zrtg3644_11_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1542:1000_1:N:0:NATGCCTT+TAATGTGT/1 77 * 0 0 * * 0 0 ATGTAAAAATTAAAAAAATTATTAATTTATTTTAATTAAATTTAAATTTTAAAATTTTAATTTTTTTATTTTAAAATTTAAATTAAAAAATATATTTATGAATTATTATATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFF,F:,,,F:F:F:FFF,::FF:FFF:FFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1542:1000_2:N:0:NATGCCTT+TAATGTGT/2 141 * 0 0 * * 0 0 TTAAAATTAAATAAAATATTTTTTAATTAATATAATAATTCATAAATATATTTTTTAATTTAAATTTTAAAATAAAAAAATTAAAATTTTAAAATTTAAATTTAATTAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_11_R1.fq.gz_G_to_A.fastq and zrtg3644_11_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1542:1000_1:N:0:NATGCCTT+TAATGTGT/1 77 * 0 0 * * 0 0 ACATAAAAATTAAAAAAACTATTAATTCATTCTAATTAAATTCAAATTCCAAAATTTTAACTTTTTTATTTTAAAATTTAAATTAAAAAACACATCCACAAACTACTATACCAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFF,F:,,,F:F:F:FFF,::FF:FFF:FFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1542:1000_2:N:0:NATGCCTT+TAATGTGT/2 141 * 0 0 * * 0 0 TTGAAGTTAAGTAGAATATTTTTTGGTTGGTATAGTAGTTTGTGGATGTGTTTTTTAATTTAAATTTTAAAATAAAAAAGTTAAAATTTTGGAATTTGAATTTAATTAGAATGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFF:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_11_R1.fq.gz_G_to_A.fastq and zrtg3644_11_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1542:1000_1:N:0:NATGCCTT+TAATGTGT/1 83 NC_047562.1_CT_converted 32907628 40 48M1D67M = 32907603 -141 GTTGGTATAGTAGTTTGTGGATGTGTTTTTTAATTTAAATTTTAAAATAAAAAAGTTAAAATTTTGGAATTTGAATTTAATTAGAATGAATTAATAGTTTTTTTAATTTTTATGT F,FFF:FFF:FF::,FFF:F:F:F,,,:F,FFF:FFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFF:F:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:16T31^A67 YS:i:-14 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1542:1000_2:N:0:NATGCCTT+TAATGTGT/2 163 NC_047562.1_CT_converted 32907603 40 73M1D41M = 32907628 141 TTGAAGTTAAGTAGAATATTTTTTGGTTGGTATAGTAGTTTGTGGATGTGTTTTTTAATTTAAATTTTAAAATAAAAAAGTTAAAATTTTGGAATTTGAATTTAATTAGAATGA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFF:F AS:i:-14 XN:i:0 XM:i:1 XO:i:1 XG:i:1 NM:i:2 MD:Z:41T31^A41 YS:i:-14 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_11_R1.fq.gz_C_to_T.fastq and zrtg3644_11_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1542:1000_1:N:0:NATGCCTT+TAATGTGT/1 77 * 0 0 * * 0 0 ATGTAAAAATTAAAAAAATTATTAATTTATTTTAATTAAATTTAAATTTTAAAATTTTAATTTTTTTATTTTAAAATTTAAATTAAAAAATATATTTATGAATTATTATATTAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:F:FFFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFF:FFF,F:,,,F:F:F:FFF,::FF:FFF:FFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1542:1000_2:N:0:NATGCCTT+TAATGTGT/2 141 * 0 0 * * 0 0 TTAAAATTAAATAAAATATTTTTTAATTAATATAATAATTCATAAATATATTTTTTAATTTAAATTTTAAAATAAAAAAATTAAAATTTTAAAATTTAAATTTAATTAAAATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF,FFFFFFFFFFFFFFFFF:FFF:F YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_11_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73335 (73.33%) aligned concordantly 0 times 11949 (11.95%) aligned concordantly exactly 1 time 14716 (14.72%) aligned concordantly >1 times 26.66% overall alignment rate 100000 reads; of these: 100000 (100.00%100000) were paired; of these: reads; of these: 73348100000 ( (73.35%) aligned concordantly 0 times100.00 % ) were paired; of these:11860 ( 11.8673188% () aligned concordantly exactly 1 time73.19 % ) aligned concordantly 0 times14792 ( 14.7911999% () aligned concordantly >1 times12.00 %26.65) aligned concordantly exactly 1 time% overall alignment rate 14813 (14.81%) aligned concordantly >1 times 26.81% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73330 (73.33%) aligned concordantly 0 times 11924 (11.92%) aligned concordantly exactly 1 time 14746 (14.75%) aligned concordantly >1 times 26.67% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_11_R1.fq.gz_C_to_T.fastq, zrtg3644_11_R1.fq.gz_G_to_A.fastq, zrtg3644_11_R2.fq.gz_C_to_T.fastq and zrtg3644_11_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60730 Mapping efficiency: 60.7% Sequence pairs with no alignments under any condition: 22750 Sequence pairs did not map uniquely: 16520 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15196 ((converted) top strand) GA/CT/CT: 15134 (complementary to (converted) top strand) GA/CT/GA: 15334 (complementary to (converted) bottom strand) CT/GA/GA: 15066 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2144414 Total methylated C's in CpG context: 28604 Total methylated C's in CHG context: 1743 Total methylated C's in CHH context: 7591 Total methylated C's in Unknown context: 74 Total unmethylated C's in CpG context: 251327 Total unmethylated C's in CHG context: 375324 Total unmethylated C's in CHH context: 1479825 Total unmethylated C's in Unknown context: 5350 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_12_R1.fq.gz to zrtg3644_12_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_12_R1.fq.gz to zrtg3644_12_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_12_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_12_R2.fq.gz to zrtg3644_12_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_12_R2.fq.gz to zrtg3644_12_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_12_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_12_R1.fq.gz_C_to_T.fastq and zrtg3644_12_R1.fq.gz_G_to_A.fastq and zrtg3644_12_R2.fq.gz_C_to_T.fastq and zrtg3644_12_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_12_R1.fq.gz_C_to_T.fastq and zrtg3644_12_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3134:1000_1:N:0:NCAAGTGG+AACATCGC/1 77 * 0 0 * * 0 0 GTTTAAGAGAAGTTTTAGGGAATAAAGAAAGGATAATTTATTAATTTTAATGTTATATATATTTATTTAAGAAATATTATGT FFFFF:F:F:FFFFFFFFFFFFF:F:FF,FFF,F,,FFFFFFF:FFFF:,FFFF:F,FFFFFFF,FFFF,:,:FF:FF:F:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3134:1000_2:N:0:NCAAGTGG+AACATCGC/2 141 * 0 0 * * 0 0 AAATAAATATATATAACATTAAAATTAATAAATTATCCTTTCTTTATTCCCTAAAACTTCTCTTAAACATTTTTATATCTTTT FF:FFFFFFFFFFF:FFFFFFFFFFFF:FF:,FF,F,,FFF:FFF,FFFF:FF::,,FF,F:FF::,,:FFFFFFF:F,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_12_R1.fq.gz_G_to_A.fastq and zrtg3644_12_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3134:1000_1:N:0:NCAAGTGG+AACATCGC/1 77 * 0 0 * * 0 0 ATTTAAAAAAAATTTTAAAAAATAAAAAAAAAATAATTTATTAATTTTAATATTATATATATTTATTTAAAAAATATTATAT FFFFF:F:F:FFFFFFFFFFFFF:F:FF,FFF,F,,FFFFFFF:FFFF:,FFFF:F,FFFFFFF,FFFF,:,:FF:FF:F:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3134:1000_2:N:0:NCAAGTGG+AACATCGC/2 141 * 0 0 * * 0 0 AAATAAATATATATAATATTAAAATTAATAAATTATTTTTTTTTTATTTTTTAAAATTTTTTTTAAATATTTTTATATTTTTT FF:FFFFFFFFFFF:FFFFFFFFFFFF:FF:,FF,F,,FFF:FFF,FFFF:FF::,,FF,F:FF::,,:FFFFFFF:F,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_12_R1.fq.gz_G_to_A.fastq and zrtg3644_12_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3134:1000_1:N:0:NCAAGTGG+AACATCGC/1 77 * 0 0 * * 0 0 ATTTAAAAAAAATTTTAAAAAATAAAAAAAAAATAATTTATTAATTTTAATATTATATATATTTATTTAAAAAATATTATAT FFFFF:F:F:FFFFFFFFFFFFF:F:FF,FFF,F,,FFFFFFF:FFFF:,FFFF:F,FFFFFFF,FFFF,:,:FF:FF:F:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3134:1000_2:N:0:NCAAGTGG+AACATCGC/2 141 * 0 0 * * 0 0 AAATAAATATATATAATATTAAAATTAATAAATTATTTTTTTTTTATTTTTTAAAATTTTTTTTAAATATTTTTATATTTTTT FF:FFFFFFFFFFF:FFFFFFFFFFFF:FF:,FF,F,,FFF:FFF,FFFF:FF::,,FF,F:FF::,,:FFFFFFF:F,FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_12_R1.fq.gz_C_to_T.fastq and zrtg3644_12_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3134:1000_1:N:0:NCAAGTGG+AACATCGC/1 83 NC_047564.1_GA_converted 58461997 3 82M = 58462011 97 ACATAATATTTCTTAAATAAATATATATAACATTAAAATTAATAAATTATCCTTTCTTTATTCCCTAAAACTTCTCTTAAAC F:F:FF:FF:,:,FFFF,FFFFFFF,F:FFFF,:FFFF:FFFFFFF,,F,FFF,FF:F:FFFFFFFFFFFFF:F:F:FFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:6C37T11A6T9A8 YS:i:-30 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:3134:1000_2:N:0:NCAAGTGG+AACATCGC/2 163 NC_047564.1_GA_converted 58462011 3 83M = 58461997 -97 AAATAAATATATATAACATTAAAATTAATAAATTATCCTTTCTTTATTCCCTAAAACTTCTCTTAAACATTTTTATATCTTTT FF:FFFFFFFFFFF:FFFFFFFFFFFF:FF:,FF,F,,FFF:FFF,FFFF:FF::,,FF,F:FF::,,:FFFFFFF:F,FFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:30T11A6T9A12C10 YS:i:-30 YT:Z:CP >>> Writing bisulfite mapping results to zrtg3644_12_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73371 (73.37%) aligned concordantly 0 times 11955 (11.96%) aligned concordantly exactly 1 time 14674 (14.67%) aligned concordantly >1 times 26.63% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73489 (73.49%) aligned concordantly 0 times 11784 (11.78%) aligned concordantly exactly 1 time 14727 (14.73%) aligned concordantly >1 times 26.51% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73217 (73.22%) aligned concordantly 0 times 11953 (11.95%) aligned concordantly exactly 1 time 14830 (10000014.83 reads; of these:% ) aligned concordantly >1 times 10000026.78 (% overall alignment rate 100.00%) were paired; of these: 73265 (73.27%) aligned concordantly 0 times 11960 (11.96%) aligned concordantly exactly 1 time 14775 (14.78%) aligned concordantly >1 times 26.73% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_12_R1.fq.gz_C_to_T.fastq, zrtg3644_12_R1.fq.gz_G_to_A.fastq, zrtg3644_12_R2.fq.gz_C_to_T.fastq and zrtg3644_12_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61267 Mapping efficiency: 61.3% Sequence pairs with no alignments under any condition: 22727 Sequence pairs did not map uniquely: 16006 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15337 ((converted) top strand) GA/CT/CT: 15464 (complementary to (converted) top strand) GA/CT/GA: 15341 (complementary to (converted) bottom strand) CT/GA/GA: 15125 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2136244 Total methylated C's in CpG context: 26364 Total methylated C's in CHG context: 1662 Total methylated C's in CHH context: 7158 Total methylated C's in Unknown context: 63 Total unmethylated C's in CpG context: 242814 Total unmethylated C's in CHG context: 360190 Total unmethylated C's in CHH context: 1498056 Total unmethylated C's in Unknown context: 5263 C methylated in CpG context: 9.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.2% Bismark completed in 0d 0h 0m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_13_R1.fq.gz to zrtg3644_13_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_13_R1.fq.gz to zrtg3644_13_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_13_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_13_R2.fq.gz to zrtg3644_13_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_13_R2.fq.gz to zrtg3644_13_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_13_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_13_R1.fq.gz_C_to_T.fastq and zrtg3644_13_R1.fq.gz_G_to_A.fastq and zrtg3644_13_R2.fq.gz_C_to_T.fastq and zrtg3644_13_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_13_R1.fq.gz_C_to_T.fastq and zrtg3644_13_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1253:1000_1:N:0:NGGTACCT+AGTCCTCA/1 77 * 0 0 * * 0 0 ATTAGTGGGGGGAGGGTGTTAATGTTTGTGGGTAGTTAAAAATTTTTTGGTTAGTGGGGGTGTAATTTTGTTGGTGGTGTAATTAAGATAAATTTAATAGATATTAAATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1253:1000_2:N:0:NGGTACCT+AGTCCTCA/2 141 * 0 0 * * 0 0 CTAATACACAATCATTTATTTAATATCTATTAAATTTATCTTAATTACACCACCAACAAAATTACACCCCCACTAACCAAAAAATTTTTAACTACCCACAAACATTAACACCCT FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:F,:::FF::F:FFF:FFFFFF,FF:,:F,::,F:F:FFFFF:F,:,:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_13_R1.fq.gz_G_to_A.fastq and zrtg3644_13_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1253:1000_1:N:0:NGGTACCT+AGTCCTCA/1 77 * 0 0 * * 0 0 ATTAATAAAAAAAAAATATTAATATTTATAAATAATTAAAAATTTTTTAATTAATAAAAACATAATTTCATTAATAATATAATTAAAATAAATTTAATAAATATTAAATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1253:1000_2:N:0:NGGTACCT+AGTCCTCA/2 141 * 0 0 * * 0 0 TTAATATATAATTATTTATTTAATATTTATTAAATTTATTTTAATTATATTATTAATGAAATTATGTTTTTATTAATTAAAAAATTTTTAATTATTTATAAATATTAATATTTT FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:F,:::FF::F:FFF:FFFFFF,FF:,:F,::,F:F:FFFFF:F,:,:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_13_R1.fq.gz_G_to_A.fastq and zrtg3644_13_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1253:1000_1:N:0:NGGTACCT+AGTCCTCA/1 77 * 0 0 * * 0 0 ATTAATAAAAAAAAAATATTAATATTTATAAATAATTAAAAATTTTTTAATTAATAAAAACATAATTTCATTAATAATATAATTAAAATAAATTTAATAAATATTAAATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1253:1000_2:N:0:NGGTACCT+AGTCCTCA/2 141 * 0 0 * * 0 0 TTAATATATAATTATTTATTTAATATTTATTAAATTTATTTTAATTATATTATTAATGAAATTATGTTTTTATTAATTAAAAAATTTTTAATTATTTATAAATATTAATATTTT FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:F,:::FF::F:FFF:FFFFFF,FF:,:F,::,F:F:FFFFF:F,:,:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_13_R1.fq.gz_C_to_T.fastq and zrtg3644_13_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1253:1000_1:N:0:NGGTACCT+AGTCCTCA/1 77 * 0 0 * * 0 0 ATTAGTGGGGGGAGGGTGTTAATGTTTGTGGGTAGTTAAAAATTTTTTGGTTAGTGGGGGTGTAATTTTGTTGGTGGTGTAATTAAGATAAATTTAATAGATATTAAATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1253:1000_2:N:0:NGGTACCT+AGTCCTCA/2 141 * 0 0 * * 0 0 CTAATACACAATCATTTATTTAATATCTATTAAATTTATCTTAATTACACCACCAACAAAATTACACCCCCACTAACCAAAAAATTTTTAACTACCCACAAACATTAACACCCT FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,:F,:::FF::F:FFF:FFFFFF,FF:,:F,::,F:F:FFFFF:F,:,:F YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_13_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73362 (73.36%) aligned concordantly 0 times 11983 (11.98%) aligned concordantly exactly 1 time 14655 (14.65%) aligned concordantly >1 times 26.64% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73448 (73.45%) aligned concordantly 0 times 11985 (11.98%) aligned concordantly exactly 1 time 14567 (14.57%) aligned concordantly >1 times 26.55% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73362 (73.36%) aligned concordantly 0 times 12002 (12.00%) aligned concordantly exactly 1 time 14636 (14.64%) aligned concordantly >1 times 26.64% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73296 (73.30%) aligned concordantly 0 times 12176 (12.18%) aligned concordantly exactly 1 time 14528 (14.53%) aligned concordantly >1 times 26.70% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_13_R1.fq.gz_C_to_T.fastq, zrtg3644_13_R1.fq.gz_G_to_A.fastq, zrtg3644_13_R2.fq.gz_C_to_T.fastq and zrtg3644_13_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61532 Mapping efficiency: 61.5% Sequence pairs with no alignments under any condition: 22553 Sequence pairs did not map uniquely: 15915 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15387 ((converted) top strand) GA/CT/CT: 15376 (complementary to (converted) top strand) GA/CT/GA: 15360 (complementary to (converted) bottom strand) CT/GA/GA: 15409 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2182732 Total methylated C's in CpG context: 28969 Total methylated C's in CHG context: 1775 Total methylated C's in CHH context: 7465 Total methylated C's in Unknown context: 87 Total unmethylated C's in CpG context: 252396 Total unmethylated C's in CHG context: 378860 Total unmethylated C's in CHH context: 1513267 Total unmethylated C's in Unknown context: 5358 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_14_R1.fq.gz to zrtg3644_14_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_14_R1.fq.gz to zrtg3644_14_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_14_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_14_R2.fq.gz to zrtg3644_14_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_14_R2.fq.gz to zrtg3644_14_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_14_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_14_R1.fq.gz_C_to_T.fastq and zrtg3644_14_R1.fq.gz_G_to_A.fastq and zrtg3644_14_R2.fq.gz_C_to_T.fastq and zrtg3644_14_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_14_R1.fq.gz_C_to_T.fastq and zrtg3644_14_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2374:1000_1:N:0:NTGGAATT+GTATTGAC/1 77 * 0 0 * * 0 0 TTAAATAAAAAAAATATTATTTTAAATGTGT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2374:1000_2:N:0:NTGGAATT+GTATTGAC/2 141 * 0 0 * * 0 0 TATTTTTTTTATTTAAAAAATATAATATTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_14_R1.fq.gz_G_to_A.fastq and zrtg3644_14_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2374:1000_1:N:0:NTGGAATT+GTATTGAC/1 77 * 0 0 * * 0 0 CTAAACAAAAAAAACATCACTTTAAACACAT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2374:1000_2:N:0:NTGGAATT+GTATTGAC/2 141 * 0 0 * * 0 0 TGTTTTTTTTGTTTAGAGAATGTAATGTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_14_R1.fq.gz_G_to_A.fastq and zrtg3644_14_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2374:1000_1:N:0:NTGGAATT+GTATTGAC/1 77 * 0 0 * * 0 0 CTAAACAAAAAAAACATCACTTTAAACACAT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2374:1000_2:N:0:NTGGAATT+GTATTGAC/2 141 * 0 0 * * 0 0 TGTTTTTTTTGTTTAGAGAATGTAATGTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_14_R1.fq.gz_C_to_T.fastq and zrtg3644_14_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2374:1000_1:N:0:NTGGAATT+GTATTGAC/1 77 * 0 0 * * 0 0 TTAAATAAAAAAAATATTATTTTAAATGTGT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2374:1000_2:N:0:NTGGAATT+GTATTGAC/2 141 * 0 0 * * 0 0 TATTTTTTTTATTTAAAAAATATAATATTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_14_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1101:27019:5509_1:N:0:TTGGAATT+GTATTGAC NC_001276.1 18117 100000 reads; of these: 100000 (100.00%) were paired; of these: 73426 (73.43%) aligned concordantly 0 times 12082 (12.08%) aligned concordantly exactly 1 time 14492 (14.49%) aligned concordantly >1 times 26.57% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73082 (73.08%) aligned concordantly 0 times 12170 (12.17%) aligned concordantly exactly 1 time 14748 (14.75%) aligned concordantly >1 times 26.92% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73602 (73.60%) aligned concordantly 0 times 11781 (11.78%) aligned concordantly exactly 1 time 14617 (14.62%) aligned concordantly >1 times 26.40% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72917 (72.92%) aligned concordantly 0 times 12297 (12.30%) aligned concordantly exactly 1 time 14786 (14.79%) aligned concordantly >1 times 27.08% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_14_R1.fq.gz_C_to_T.fastq, zrtg3644_14_R1.fq.gz_G_to_A.fastq, zrtg3644_14_R2.fq.gz_C_to_T.fastq and zrtg3644_14_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61819 Mapping efficiency: 61.8% Sequence pairs with no alignments under any condition: 22067 Sequence pairs did not map uniquely: 16114 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15417 ((converted) top strand) GA/CT/CT: 15428 (complementary to (converted) top strand) GA/CT/GA: 15748 (complementary to (converted) bottom strand) CT/GA/GA: 15225 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2175796 Total methylated C's in CpG context: 32848 Total methylated C's in CHG context: 1890 Total methylated C's in CHH context: 7753 Total methylated C's in Unknown context: 82 Total unmethylated C's in CpG context: 247090 Total unmethylated C's in CHG context: 376369 Total unmethylated C's in CHH context: 1509846 Total unmethylated C's in Unknown context: 5246 C methylated in CpG context: 11.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_15_R1.fq.gz to zrtg3644_15_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_15_R1.fq.gz to zrtg3644_15_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_15_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_15_R2.fq.gz to zrtg3644_15_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_15_R2.fq.gz to zrtg3644_15_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_15_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_15_R1.fq.gz_C_to_T.fastq and zrtg3644_15_R1.fq.gz_G_to_A.fastq and zrtg3644_15_R2.fq.gz_C_to_T.fastq and zrtg3644_15_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_15_R1.fq.gz_C_to_T.fastq and zrtg3644_15_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2157:1000_1:N:0:NCTCTACA+AGGAGGTA/1 99 NC_047563.1_CT_converted 50142193 0 24M1I73M1I15M = 50142257 191 ATAGAATAAAATATTATTTTATGGTTTTTTTAATTTTAAATATGAATTAAGGTATGTGTGTTTATAATATTTATGTGTTATTATTGTTTATTTTATTTGTTTTTATATTTTTAT FFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFF,F,FFFFFF:FFFFF:FFFF::FFFFFFFFFFF:FFFFF AS:i:-28 XS:i:-28 XN:i:0 XM:i:2 XO:i:2 XG:i:2 NM:i:4 MD:Z:58T51T1 YS:i:-67 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2157:1000_2:N:0:NCTCTACA+AGGAGGTA/2 147 NC_047563.1_CT_converted 50142257 0 33M1I8M14D72M = 50142193 -191 AATATTTATGTGTTATTATTGTTTATTTTATTTGTTTTTATATTTTTATATGGATTTTGGAATATTTTGAATTTTTTTTATTTAATTGATGTTTATTTATAGTTTTGTTTTTGA FFF:FF:FFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF,FFFFFFFFF: AS:i:-67 XS:i:-65 XN:i:0 XM:i:2 XO:i:2 XG:i:15 NM:i:17 MD:Z:41^TTTTTTTGGAATAT60G4A6 YS:i:-28 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_15_R1.fq.gz_G_to_A.fastq and zrtg3644_15_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2157:1000_1:N:0:NCTCTACA+AGGAGGTA/1 77 * 0 0 * * 0 0 ATAAAATAAAATATTATTTTATAATTTTTTTAATTTTAAATATAAATTAAAATATATATATTTATAATATTTATATATTATTATTATTTATTTTATTTATTTTTATATTTTTAT FFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFF,F,FFFFFF:FFFFF:FFFF::FFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2157:1000_2:N:0:NCTCTACA+AGGAGGTA/2 141 * 0 0 * * 0 0 TTAAAAATAAAATTATAAATAAATATTAATTAAATAAAAAAAATTTAAAATATTTTAAAATTTATATAAAAATATAAAAATAAATAAAATAAATAATAATAATATATAAATATT :FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_15_R1.fq.gz_G_to_A.fastq and zrtg3644_15_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2157:1000_1:N:0:NCTCTACA+AGGAGGTA/1 77 * 0 0 * * 0 0 ATAAAATAAAATATTATTTTATAATTTTTTTAATTTTAAATATAAATTAAAATATATATATTTATAATATTTATATATTATTATTATTTATTTTATTTATTTTTATATTTTTAT FFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFF:FFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFF,F,FFFFFF:FFFFF:FFFF::FFFFFFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2157:1000_2:N:0:NCTCTACA+AGGAGGTA/2 141 * 0 0 * * 0 0 TTAAAAATAAAATTATAAATAAATATTAATTAAATAAAAAAAATTTAAAATATTTTAAAATTTATATAAAAATATAAAAATAAATAAAATAAATAATAATAATATATAAATATT :FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF:FFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_15_R1.fq.gz_C_to_T.fastq and zrtg3644_15_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2157:1000_1:N:0:NCTCTACA+AGGAGGTA/1 83 NC_047561.1_GA_converted 33259345 2 83M1I30M = 33259266 -192 ATAAAAATATAAAAACAAATAAAATAAACAATAATAACACATAAATATTATAAACACACATACCTTAATTCATATTTAAAATTAAAAAAACCATAAAATAATATTTTATTCTAT FFFFF:FFFFFFFFFFF::FFFF:FFFFF:FFFFFF,F,FFFFFFFFFFFFFFFFFFF,:FFFFFFFFFFFFFF:FFFFFFFFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFF AS:i:-26 XS:i:-28 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:1A52A44C13 YS:i:-53 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2157:1000_2:N:0:NCTCTACA+AGGAGGTA/2 163 NC_047561.1_GA_converted 33259266 2 67M14D47M = 33259345 192 TCAAAAACAAAACTATAAATAAACATCAATTAAATAAAAAAAATTCAAAATATTCCAAAATCCATATAAAAATATAAAAACAAATAAAATAAACAATAATAACACATAAATATT :FFFFFFFFF,FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFF:FF:FFF AS:i:-53 XS:i:-53 XN:i:0 XM:i:1 XO:i:1 XG:i:14 NM:i:15 MD:Z:6T60^AAAAAATATTTCAA47 YS:i:-26 YT:Z:CP >>> Writing bisulfite mapping results to zrtg3644_15_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73539 (73.54100000% reads; of these:) aligned concordantly 0 times 10000011836 ( (11.84%) aligned concordantly exactly 1 time100.00 % ) were paired; of these:14625 ( 14.6273282% () aligned concordantly >1 times73.28 %26.46) aligned concordantly 0 times% overall alignment rate 12099 (12.10%) aligned concordantly exactly 1 time 14619 (14.62%) aligned concordantly >1 times 26.72% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73314 (73.31%) aligned concordantly 0 times 12083 (12.08%) aligned concordantly exactly 1 time 14603 (14.60%) aligned concordantly >1 times 26.69% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73361 (73.36%) aligned concordantly 0 times 11999 (12.00%) aligned concordantly exactly 1 time 14640 (14.64%) aligned concordantly >1 times 26.64% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_15_R1.fq.gz_C_to_T.fastq, zrtg3644_15_R1.fq.gz_G_to_A.fastq, zrtg3644_15_R2.fq.gz_C_to_T.fastq and zrtg3644_15_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61239 Mapping efficiency: 61.2% Sequence pairs with no alignments under any condition: 22623 Sequence pairs did not map uniquely: 16138 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15050 ((converted) top strand) GA/CT/CT: 15411 (complementary to (converted) top strand) GA/CT/GA: 15393 (complementary to (converted) bottom strand) CT/GA/GA: 15385 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2167128 Total methylated C's in CpG context: 31015 Total methylated C's in CHG context: 1869 Total methylated C's in CHH context: 7405 Total methylated C's in Unknown context: 79 Total unmethylated C's in CpG context: 248991 Total unmethylated C's in CHG context: 374914 Total unmethylated C's in CHH context: 1502934 Total unmethylated C's in Unknown context: 5256 C methylated in CpG context: 11.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_16_R1.fq.gz to zrtg3644_16_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_16_R1.fq.gz to zrtg3644_16_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_16_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_16_R2.fq.gz to zrtg3644_16_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_16_R2.fq.gz to zrtg3644_16_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_16_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_16_R1.fq.gz_C_to_T.fastq and zrtg3644_16_R1.fq.gz_G_to_A.fastq and zrtg3644_16_R2.fq.gz_C_to_T.fastq and zrtg3644_16_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_16_R1.fq.gz_C_to_T.fastq and zrtg3644_16_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1470:1000_1:N:0:NGAGCGTG+ACTTACGG/1 99 NC_047567.1_CT_converted 14590834 42 112M = 14590862 141 TAGAATTGTTTAATTTGTTTATTGTATTGTAAATTTTTGTGTTGAAAATTTGTGTATTGTTTATTGATGATGTTTTTTTATTTTTTAAGTTTTTTTAGTTTTGTTTTGTATT FFFFFFFFFFFFFFFFFFF:FFFFFF:F,FFFF:FFFFFFFFFFFFF:FFFFFF:F:FFFFFFFFFFFF,F,FFFFF,FFFFFFFFFFFFFF,:FFF:::,FFFFFF,FFFF AS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:77G14G16G2 YS:i:-6 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1470:1000_2:N:0:NGAGCGTG+ACTTACGG/2 147 NC_047567.1_CT_converted 14590862 42 113M = 14590834 -141 GTAAATTTTTGTGTTGAAAATTTGTGTATTGTTTATTGATGATGTTTTTGTATTTTTTAAGTTTGTTTAGTTTTGTTTTGTATTAAGTTGGTAGTGGGTATAGTGGGTTGTGA FFFFFFFFFFFF:F:FFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFF,FFFFFF::FFFFF:FFFFFF,FFF:,FFF,FFFF,FFFFFFF::FF:FFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:81G31 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_16_R1.fq.gz_G_to_A.fastq and zrtg3644_16_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1470:1000_1:N:0:NGAGCGTG+ACTTACGG/1 77 * 0 0 * * 0 0 TAAAATTATTTAATTTATTTATTATATTATAAATTTTTATATTAAAAATTTATATATTATTTATTAATAATATTTTTTTATTTTTTAAATTTTTTTAATTTTATTTTATATT FFFFFFFFFFFFFFFFFFF:FFFFFF:F,FFFF:FFFFFFFFFFFFF:FFFFFF:F:FFFFFFFFFFFF,F,FFFFF,FFFFFFFFFFFFFF,:FFF:::,FFFFFF,FFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1470:1000_2:N:0:NGAGCGTG+ACTTACGG/2 141 * 0 0 * * 0 0 TTATAATTTATTATATTTATTATTAATTTAATATAAAATAAAATTAAATAAATTTAAAAAATATAAAAATATTATTAATAAATAATATATAAATTTTTAATATAAAAATTTAT FFFFFFFFFFFFFFFF:FF::FFFFFFF,FFFF,FFF,:FFF,FFFFFF:FFFFF::FFFFFF,FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_16_R1.fq.gz_G_to_A.fastq and zrtg3644_16_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1470:1000_1:N:0:NGAGCGTG+ACTTACGG/1 77 * 0 0 * * 0 0 TAAAATTATTTAATTTATTTATTATATTATAAATTTTTATATTAAAAATTTATATATTATTTATTAATAATATTTTTTTATTTTTTAAATTTTTTTAATTTTATTTTATATT FFFFFFFFFFFFFFFFFFF:FFFFFF:F,FFFF:FFFFFFFFFFFFF:FFFFFF:F:FFFFFFFFFFFF,F,FFFFF,FFFFFFFFFFFFFF,:FFF:::,FFFFFF,FFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1470:1000_2:N:0:NGAGCGTG+ACTTACGG/2 141 * 0 0 * * 0 0 TTATAATTTATTATATTTATTATTAATTTAATATAAAATAAAATTAAATAAATTTAAAAAATATAAAAATATTATTAATAAATAATATATAAATTTTTAATATAAAAATTTAT FFFFFFFFFFFFFFFF:FF::FFFFFFF,FFFF,FFF,:FFF,FFFFFF:FFFFF::FFFFFF,FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_16_R1.fq.gz_C_to_T.fastq and zrtg3644_16_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1470:1000_1:N:0:NGAGCGTG+ACTTACGG/1 83 NC_047561.1_GA_converted 13314204 23 112M = 13314175 -141 AATACAAAACAAAACTAAAAAAACTTAAAAAATAAAAAAACATCATCAATAAACAATACACAAATTTTCAACACAAAAATTTACAATACAATAAACAAATTAAACAATTCTA FFFF,FFFFFF,:::FFF:,FFFFFFFFFFFFFF,FFFFF,F,FFFFFFFFFFFF:F:FFFFFF:FFFFFFFFFFFFF:FFFF,F:FFFFFF:FFFFFFFFFFFFFFFFFFF AS:i:-42 XN:i:0 XM:i:7 XO:i:0 XG:i:0 NM:i:7 MD:Z:2C16C14C31A2T16C17A7 YS:i:-24 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1470:1000_2:N:0:NGAGCGTG+ACTTACGG/2 163 NC_047561.1_GA_converted 13314175 23 113M = 13314204 141 TCACAACCCACTATACCCACTACCAACTTAATACAAAACAAAACTAAACAAACTTAAAAAATACAAAAACATCATCAATAAACAATACACAAATTTTCAACACAAAAATTTAC FFFFFFFFFFFFFFFF:FF::FFFFFFF,FFFF,FFF,:FFF,FFFFFF:FFFFF::FFFFFF,FFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFF:F:FFFFFFFFFFFF AS:i:-24 XN:i:0 XM:i:4 XO:i:0 XG:i:0 NM:i:4 MD:Z:13A17C63A2T14 YS:i:-42 YT:Z:CP >>> Writing bisulfite mapping results to zrtg3644_16_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72968 (72.97%) aligned concordantly 0 times 12170 (12.17%) aligned concordantly exactly 1 time 14862 (14.86%) aligned concordantly >1 times 27.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73296 (73.30%) aligned concordantly 0 times 11792 (11.79%) aligned concordantly exactly 1 time 14912 (14.91%) aligned concordantly >1 times 26.70% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72370 (72.37%) aligned concordantly 0 times 12255 (12.26%) aligned concordantly exactly 1 time 15375 (15.38%) aligned concordantly >1 times 27.63% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72338 (72.34%) aligned concordantly 0 times 12256 (12.26%) aligned concordantly exactly 1 time 15406 (15.41%) aligned concordantly >1 times 27.66% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_16_R1.fq.gz_C_to_T.fastq, zrtg3644_16_R1.fq.gz_G_to_A.fastq, zrtg3644_16_R2.fq.gz_C_to_T.fastq and zrtg3644_16_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61417 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 21411 Sequence pairs did not map uniquely: 17172 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15314 ((converted) top strand) GA/CT/CT: 15456 (complementary to (converted) top strand) GA/CT/GA: 15634 (complementary to (converted) bottom strand) CT/GA/GA: 15013 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2145277 Total methylated C's in CpG context: 29412 Total methylated C's in CHG context: 1874 Total methylated C's in CHH context: 7534 Total methylated C's in Unknown context: 72 Total unmethylated C's in CpG context: 251689 Total unmethylated C's in CHG context: 374150 Total unmethylated C's in CHH context: 1480618 Total unmethylated C's in Unknown context: 5061 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_17_R1.fq.gz to zrtg3644_17_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_17_R1.fq.gz to zrtg3644_17_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_17_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_17_R2.fq.gz to zrtg3644_17_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_17_R2.fq.gz to zrtg3644_17_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_17_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_17_R1.fq.gz_C_to_T.fastq and zrtg3644_17_R1.fq.gz_G_to_A.fastq and zrtg3644_17_R2.fq.gz_C_to_T.fastq and zrtg3644_17_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_17_R1.fq.gz_C_to_T.fastq and zrtg3644_17_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1759:1000_1:N:0:NAAGCATC+AATGGATT/1 77 * 0 0 * * 0 0 AAATTAAATATTATAATTAAATATTATTATATTAATTTTTATATTTATTATTTAATTAATTTATTAAATTTATAAAATTATATATTTATAATTTATATTATTAAAAAAATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFF:FF:FFFF:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1759:1000_2:N:0:NAAGCATC+AATGGATT/2 141 * 0 0 * * 0 0 TATATTTTATTAAATATTTTTTTAATAATATAAATTATAAATATATAATTTTATAAATTTAATAAATTAATTAAATAATAAATATAAAAATTAATATAATAATATTTAATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_17_R1.fq.gz_G_to_A.fastq and zrtg3644_17_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1759:1000_1:N:0:NAAGCATC+AATGGATT/1 77 * 0 0 * * 0 0 AAATTAAACATCACAATTAAACACCATTACATTAATTTCTACATCCATTATTTAATCAACCTATCAAATTCACAAAATTATATATTTATAATCTACACTACTAAAAAAATACCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFF:FF:FFFF:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1759:1000_2:N:0:NAAGCATC+AATGGATT/2 141 * 0 0 * * 0 0 TATATTTTGTTGGGTATTTTTTTAGTAGTGTAGATTATAAATATATAATTTTGTGAATTTGATAGGTTGATTAAATAATGGATGTAGAAATTAATGTAATGGTGTTTAATTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_17_R1.fq.gz_G_to_A.fastq and zrtg3644_17_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1759:1000_1:N:0:NAAGCATC+AATGGATT/1 77 * 0 0 * * 0 0 AAATTAAACATCACAATTAAACACCATTACATTAATTTCTACATCCATTATTTAATCAACCTATCAAATTCACAAAATTATATATTTATAATCTACACTACTAAAAAAATACCC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFF:FF:FFFF:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1759:1000_2:N:0:NAAGCATC+AATGGATT/2 141 * 0 0 * * 0 0 TATATTTTGTTGGGTATTTTTTTAGTAGTGTAGATTATAAATATATAATTTTGTGAATTTGATAGGTTGATTAAATAATGGATGTAGAAATTAATGTAATGGTGTTTAATTGT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_17_R1.fq.gz_C_to_T.fastq and zrtg3644_17_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1759:1000_1:N:0:NAAGCATC+AATGGATT/1 77 * 0 0 * * 0 0 AAATTAAATATTATAATTAAATATTATTATATTAATTTTTATATTTATTATTTAATTAATTTATTAAATTTATAAAATTATATATTTATAATTTATATTATTAAAAAAATATTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFF:FFFF:FF:FFFF:F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1759:1000_2:N:0:NAAGCATC+AATGGATT/2 141 * 0 0 * * 0 0 TATATTTTATTAAATATTTTTTTAATAATATAAATTATAAATATATAATTTTATAAATTTAATAAATTAATTAAATAATAAATATAAAAATTAATATAATAATATTTAATTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFF:FF:FF:FFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_17_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72780 (72.78%) aligned concordantly 0 times 12221 (12.22%) aligned concordantly exactly 1 time 14999 (15.00%) aligned concordantly >1 times 27.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72890 (72.89%) aligned concordantly 0 times 12135 (12.13%) aligned concordantly exactly 1 time 14975 (14.97%) aligned concordantly >1 times 10000027.11 reads; of these:% overall alignment rate 100000 (100.00%) were paired; of these: 72687 (72.69%) aligned concordantly 0 times 12318 (12.32%) aligned concordantly exactly 1 time 14995 (14.99%) aligned concordantly >1 times 27.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72740 (72.74%) aligned concordantly 0 times 12143 (12.14%) aligned concordantly exactly 1 time 15117 (15.12%) aligned concordantly >1 times 27.26% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_17_R1.fq.gz_C_to_T.fastq, zrtg3644_17_R1.fq.gz_G_to_A.fastq, zrtg3644_17_R2.fq.gz_C_to_T.fastq and zrtg3644_17_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61619 Mapping efficiency: 61.6% Sequence pairs with no alignments under any condition: 21382 Sequence pairs did not map uniquely: 16999 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15152 ((converted) top strand) GA/CT/CT: 15598 (complementary to (converted) top strand) GA/CT/GA: 15386 (complementary to (converted) bottom strand) CT/GA/GA: 15483 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2189226 Total methylated C's in CpG context: 29704 Total methylated C's in CHG context: 1910 Total methylated C's in CHH context: 7729 Total methylated C's in Unknown context: 73 Total unmethylated C's in CpG context: 261477 Total unmethylated C's in CHG context: 384145 Total unmethylated C's in CHH context: 1504261 Total unmethylated C's in Unknown context: 5167 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_18_R1.fq.gz to zrtg3644_18_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_18_R1.fq.gz to zrtg3644_18_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_18_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_18_R2.fq.gz to zrtg3644_18_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_18_R2.fq.gz to zrtg3644_18_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_18_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_18_R1.fq.gz_C_to_T.fastq and zrtg3644_18_R1.fq.gz_G_to_A.fastq and zrtg3644_18_R2.fq.gz_C_to_T.fastq and zrtg3644_18_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_18_R1.fq.gz_C_to_T.fastq and zrtg3644_18_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1741:1000_1:N:0:NCTTCAAG+TTCATGGT/1 77 * 0 0 * * 0 0 TAATAATAATAATTTTTATATTTTATTAAATTATTTATATTAATTAAATTAATTAATTATTATTATATATAATTTTATAATTAAAATATTAAATTTATAAATTATAAATTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1741:1000_2:N:0:NCTTCAAG+TTCATGGT/2 141 * 0 0 * * 0 0 ATATATAAATTAAAATAAAAAATTATAATTTTAAAAAATTTAATAAATATAAAAAAAATTTTAAATAAATTTAAATTTATAATTTATAATTTATAAATTTAATATTTTAATTAT :FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF:FFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_18_R1.fq.gz_G_to_A.fastq and zrtg3644_18_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1741:1000_1:N:0:NCTTCAAG+TTCATGGT/1 77 * 0 0 * * 0 0 TAACAATAACAATTTTCATATTTTATTAAACTATTTATATCAATCAAACTAATTAACTATCATCATATATAACTCTATAATTAAAATATCAAACTTATAAACCACAAATTACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1741:1000_2:N:0:NCTTCAAG+TTCATGGT/2 141 * 0 0 * * 0 0 ATATGTAAATTAGGATGAAAAATTATGATTTTAAAAAATTTAATAAATATGAAAAAAGTTTTAGATGGATTTGAATTTGTAATTTGTGGTTTATAAGTTTGATATTTTAATTAT :FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF:FFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_18_R1.fq.gz_G_to_A.fastq and zrtg3644_18_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1741:1000_1:N:0:NCTTCAAG+TTCATGGT/1 77 * 0 0 * * 0 0 TAACAATAACAATTTTCATATTTTATTAAACTATTTATATCAATCAAACTAATTAACTATCATCATATATAACTCTATAATTAAAATATCAAACTTATAAACCACAAATTACA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1741:1000_2:N:0:NCTTCAAG+TTCATGGT/2 141 * 0 0 * * 0 0 ATATGTAAATTAGGATGAAAAATTATGATTTTAAAAAATTTAATAAATATGAAAAAAGTTTTAGATGGATTTGAATTTGTAATTTGTGGTTTATAAGTTTGATATTTTAATTAT :FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF:FFFFFFFFFFFF:FFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_18_R1.fq.gz_C_to_T.fastq and zrtg3644_18_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1741:1000_1:N:0:NCTTCAAG+TTCATGGT/1 77 * 0 0 * * 0 0 TAATAATAATAATTTTTATATTTTATTAAATTATTTATATTAATTAAATTAATTAATTATTATTATATATAATTTTATAATTAAAATATTAAATTTATAAATTATAAATTATA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF:FFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1741:1000_2:N:0:NCTTCAAG+TTCATGGT/2 141 * 0 0 * * 0 0 ATATATAAATTAAAATAAAAAATTATAATTTTAAAAAATTTAATAAATATAAAAAAAATTTTAAATAAATTTAAATTTATAATTTATAATTTATAAATTTAATATTTTAATTAT :FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFF:,FFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFFFF:FFFFFFFFFFFF:FFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_18_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72778 (72.78%) aligned concordantly 0 times 12419 (12.42%) aligned concordantly exactly 1 time 14803 (14.80%) aligned concordantly >1 times 27.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73326 (73.33%) aligned concordantly 0 times 12206 (12.21%) aligned concordantly exactly 1 time 14468 (14.47%) aligned concordantly >1 times 26.67% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72968 (72.97%) aligned concordantly 0 times 12301 (12.30%) aligned concordantly exactly 1 time 14731 (14.73%) aligned concordantly >1 times 27.03% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73080 (73.08%) aligned concordantly 0 times 12476 (12.48%) aligned concordantly exactly 1 time 14444 (14.44%) aligned concordantly >1 times 26.92% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_18_R1.fq.gz_C_to_T.fastq, zrtg3644_18_R1.fq.gz_G_to_A.fastq, zrtg3644_18_R2.fq.gz_C_to_T.fastq and zrtg3644_18_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 62205 Mapping efficiency: 62.2% Sequence pairs with no alignments under any condition: 21452 Sequence pairs did not map uniquely: 16343 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15450 ((converted) top strand) GA/CT/CT: 15675 (complementary to (converted) top strand) GA/CT/GA: 15522 (complementary to (converted) bottom strand) CT/GA/GA: 15558 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2196700 Total methylated C's in CpG context: 29864 Total methylated C's in CHG context: 1818 Total methylated C's in CHH context: 7786 Total methylated C's in Unknown context: 71 Total unmethylated C's in CpG context: 258905 Total unmethylated C's in CHG context: 385573 Total unmethylated C's in CHH context: 1512754 Total unmethylated C's in Unknown context: 5230 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.3% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_19_R1.fq.gz to zrtg3644_19_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_19_R1.fq.gz to zrtg3644_19_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_19_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_19_R2.fq.gz to zrtg3644_19_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_19_R2.fq.gz to zrtg3644_19_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_19_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_19_R1.fq.gz_C_to_T.fastq and zrtg3644_19_R1.fq.gz_G_to_A.fastq and zrtg3644_19_R2.fq.gz_C_to_T.fastq and zrtg3644_19_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_19_R1.fq.gz_C_to_T.fastq and zrtg3644_19_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1615:1000_1:N:0:NCAGAAGG+TATGATGG/1 77 * 0 0 * * 0 0 TGTTTATTTTTTATAATTATTATTAAAAAAAATAATAATAATTTTGAATTTTTTTAAAATTTATATATATATAATTATATTAAATATTTATAAATAATTTTAAAATATTTTTA FFFFFFFFFFFF::FF:,:FF::FFF:FFFFFFFFF:FFFFFFFFFFFF:F:FFFFFF:FFF:FF,F:FFF:,FFFFFFFFFF:FFFFFF,FFFF:F:FFF::FFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1615:1000_2:N:0:NCAGAAGG+TATGATGG/2 141 * 0 0 * * 0 0 TTTAAAAATATTTTAAAATTATTTATAAATATTTAATATAATTATATATATATAAATTTTAAAAAAATTCAAAATTATTATTATTTTTTTTAATAATAATTATAAAAAATAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_19_R1.fq.gz_G_to_A.fastq and zrtg3644_19_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1615:1000_1:N:0:NCAGAAGG+TATGATGG/1 99 NC_047568.1_GA_converted 39689236 42 113M = 39689237 115 CATTCATTTTCTACAACCACTATCAAAAAAAATAATAATAACCTCAAATTTCTTCAAAATTCATACATACATAATTATATCAAATATTTACAAATAACTTTAAAACACTTTTA FFFFFFFFFFFF::FF:,:FF::FFF:FFFFFFFFF:FFFFFFFFFFFF:F:FFFFFF:FFF:FF,F:FFF:,FFFFFFFFFF:FFFFFF,FFFF:F:FFF::FFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:41T71 YS:i:-6 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1615:1000_2:N:0:NCAGAAGG+TATGATGG/2 147 NC_047568.1_GA_converted 39689237 42 114M = 39689236 -115 ATTCATTTTCTACAACCACTATCAAAAAAAATAATAATAACCTCAAATTTCTTCAAAATTCATACATACATAATTATATCAAATATTTACAAATAACTTTAAAACACTTTTAAA FFFFF:FFF:FFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF:FF,FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:40T73 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_19_R1.fq.gz_G_to_A.fastq and zrtg3644_19_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1615:1000_1:N:0:NCAGAAGG+TATGATGG/1 77 * 0 0 * * 0 0 CATTCATTTTCTACAACCACTATCAAAAAAAATAATAATAACCTCAAATTTCTTCAAAATTCATACATACATAATTATATCAAATATTTACAAATAACTTTAAAACACTTTTA FFFFFFFFFFFF::FF:,:FF::FFF:FFFFFFFFF:FFFFFFFFFFFF:F:FFFFFF:FFF:FF,F:FFF:,FFFFFFFFFF:FFFFFF,FFFF:F:FFF::FFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1615:1000_2:N:0:NCAGAAGG+TATGATGG/2 141 * 0 0 * * 0 0 TTTAAAAGTGTTTTAAAGTTATTTGTAAATATTTGATATAATTATGTATGTATGAATTTTGAAGAAATTTGAGGTTATTATTATTTTTTTTGATAGTGGTTGTAGAAAATGAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFF:FFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_19_R1.fq.gz_C_to_T.fastq and zrtg3644_19_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1615:1000_1:N:0:NCAGAAGG+TATGATGG/1 77 * 0 0 * * 0 0 TGTTTATTTTTTATAATTATTATTAAAAAAAATAATAATAATTTTGAATTTTTTTAAAATTTATATATATATAATTATATTAAATATTTATAAATAATTTTAAAATATTTTTA FFFFFFFFFFFF::FF:,:FF::FFF:FFFFFFFFF:FFFFFFFFFFFF:F:FFFFFF:FFF:FF,F:FFF:,FFFFFFFFFF:FFFFFF,FFFF:F:FFF::FFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1615:1000_2:N:0:NCAGAAGG+TATGATGG/2 141 * 0 0 * * 0 0 TTTAAAAATATTTTAAAATTATTTATAAATATTTAATATAATTATATATATATAAATTTTAAAAAAATTCAAAATTATTATTATTTTTTTTAATAATAATTATAAAAAATAAAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FF:FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFF:FFF:FFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_19_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73171 (73.17%) aligned concordantly 0 times 12055 (12.05%) aligned concordantly exactly 1 time 14774 (14.77%) aligned concordantly >1 times 26.83% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72965 (72.97%) aligned concordantly 0 times 11925 (11.93%) aligned concordantly exactly 1 time 15110 (15.11%) aligned concordantly >1 times 27.04% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73352 (73.35%) aligned concordantly 0 times 11615 (11.62%) aligned concordantly exactly 1 time 15033 (15.03%) aligned concordantly >1 times 26.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73238 (73.24%) aligned concordantly 0 times 12126 (12.13%) aligned concordantly exactly 1 time 14636 (14.64%) aligned concordantly >1 times 26.76% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_19_R1.fq.gz_C_to_T.fastq, zrtg3644_19_R1.fq.gz_G_to_A.fastq, zrtg3644_19_R2.fq.gz_C_to_T.fastq and zrtg3644_19_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61076 Mapping efficiency: 61.1% Sequence pairs with no alignments under any condition: 22233 Sequence pairs did not map uniquely: 16691 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 14959 ((converted) top strand) GA/CT/CT: 15367 (complementary to (converted) top strand) GA/CT/GA: 15363 (complementary to (converted) bottom strand) CT/GA/GA: 15387 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2148194 Total methylated C's in CpG context: 27784 Total methylated C's in CHG context: 1793 Total methylated C's in CHH context: 7536 Total methylated C's in Unknown context: 53 Total unmethylated C's in CpG context: 250625 Total unmethylated C's in CHG context: 372639 Total unmethylated C's in CHH context: 1487817 Total unmethylated C's in Unknown context: 5360 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.0% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_1_R1.fq.gz to zrtg3644_1_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_1_R1.fq.gz to zrtg3644_1_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_1_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_1_R2.fq.gz to zrtg3644_1_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_1_R2.fq.gz to zrtg3644_1_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_1_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_1_R1.fq.gz_C_to_T.fastq and zrtg3644_1_R1.fq.gz_G_to_A.fastq and zrtg3644_1_R2.fq.gz_C_to_T.fastq and zrtg3644_1_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_1_R1.fq.gz_C_to_T.fastq and zrtg3644_1_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2049:1000_1:N:0:NGTTGCGA+TTGCTCTA/1 77 * 0 0 * * 0 0 TAAATTTTTATTAATAATAATAATAATATTTTAATAAATAAAAAAATATTTATATATATTTTTTAAAATTTTATATAAAATAAATATTAATTAAAATAAATTTATTTTTTATAT FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2049:1000_2:N:0:NGTTGCGA+TTGCTCTA/2 141 * 0 0 * * 0 0 TATAATATATAAAAAATAAATTTATTTTAATTAATATTTATTTTATATAAAATTTTAAAAAATATATATAAATATTTTTTTATTTATTAAAATATTATTATTATTATTAATAAA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFF:FFFFF:F:FFFF:FFF:FFFFFFF,:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_1_R1.fq.gz_G_to_A.fastq and zrtg3644_1_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2049:1000_1:N:0:NGTTGCGA+TTGCTCTA/1 99 NC_047560.1_GA_converted 10931927 23 114M = 10931933 120 TAAATTTTTACCAATAACAACAACAACATCTCAACAAATAAAAAAACATTCACACATATCTTTTAAAATCTCATATAAAACAAACACTAATTAAAACAAACTTACCCCCTATAC FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:12T42C0A19C27A9 YS:i:-30 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2049:1000_2:N:0:NGTTGCGA+TTGCTCTA/2 147 NC_047560.1_GA_converted 10931933 23 114M = 10931927 -120 TTTACCAATAACAACAACAACATCTCAACAAATAAAAAAACATTCACACATATCTTTTAAAATCTCATATAAAACAAACACTAATTAAAACAAACTTACCCCCTATACATTATA FFFFFF:,FFFFFFF:FFF:FFFF:F:FFFFF:FFFFFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:6T42C0A19C27A15 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_1_R1.fq.gz_G_to_A.fastq and zrtg3644_1_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2049:1000_1:N:0:NGTTGCGA+TTGCTCTA/1 83 NC_047560.1_CT_converted 2448361 23 114M = 2448355 -120 GTATAGGGGGTAAGTTTGTTTTAATTAGTGTTTGTTTTATATGAGATTTTAAAAGATATGTGTGAATGTTTTTTTATTTGTTGAGATGTTGTTGTTGTTATTGGTAAAAATTTA FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:9T27G19T0G42A12 YS:i:-30 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2049:1000_2:N:0:NGTTGCGA+TTGCTCTA/2 163 NC_047560.1_CT_converted 2448355 23 114M = 2448361 120 TATAATGTATAGGGGGTAAGTTTGTTTTAATTAGTGTTTGTTTTATATGAGATTTTAAAAGATATGTGTGAATGTTTTTTTATTTGTTGAGATGTTGTTGTTGTTATTGGTAAA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFF:FFFFF:F:FFFF:FFF:FFFFFFF,:FFFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:15T27G19T0G42A6 YS:i:-30 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_1_R1.fq.gz_C_to_T.fastq and zrtg3644_1_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2049:1000_1:N:0:NGTTGCGA+TTGCTCTA/1 77 * 0 0 * * 0 0 TAAATTTTTATTAATAATAATAATAATATTTTAATAAATAAAAAAATATTTATATATATTTTTTAAAATTTTATATAAAATAAATATTAATTAAAATAAATTTATTTTTTATAT FFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2049:1000_2:N:0:NGTTGCGA+TTGCTCTA/2 141 * 0 0 * * 0 0 TATAATATATAAAAAATAAATTTATTTTAATTAATATTTATTTTATATAAAATTTTAAAAAATATATATAAATATTTTTTTATTTATTAAAATATTATTATTATTATTAATAAA FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFFFFF:FFFFF:F:FFFF:FFF:FFFFFFF,:FFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_1_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72780 (72.78%) aligned concordantly 0 times 12122 (12.12%) aligned concordantly exactly 1 time 15098 (15.10%) aligned concordantly >1 times 27.22% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72694 (72.69%) aligned concordantly 0 times 12351 (12.35%) aligned concordantly exactly 1 time 14955 (14.96%) aligned concordantly >1 times 27.31% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72922 (72.92%) aligned concordantly 0 times 12192 (12.19%) aligned concordantly exactly 1 time 14886 (14.89%) aligned concordantly >1 times 27.08% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72965 (72.97%) aligned concordantly 0 times 12217 (12.22%) aligned concordantly exactly 1 time 14818 (14.82%) aligned concordantly >1 times 27.04% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_1_R1.fq.gz_C_to_T.fastq, zrtg3644_1_R1.fq.gz_G_to_A.fastq, zrtg3644_1_R2.fq.gz_C_to_T.fastq and zrtg3644_1_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 62198 Mapping efficiency: 62.2% Sequence pairs with no alignments under any condition: 21145 Sequence pairs did not map uniquely: 16657 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15499 ((converted) top strand) GA/CT/CT: 15602 (complementary to (converted) top strand) GA/CT/GA: 15419 (complementary to (converted) bottom strand) CT/GA/GA: 15678 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2196915 Total methylated C's in CpG context: 26894 Total methylated C's in CHG context: 1757 Total methylated C's in CHH context: 6890 Total methylated C's in Unknown context: 64 Total unmethylated C's in CpG context: 260090 Total unmethylated C's in CHG context: 385093 Total unmethylated C's in CHH context: 1516191 Total unmethylated C's in Unknown context: 5477 C methylated in CpG context: 9.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.2% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_20_R1.fq.gz to zrtg3644_20_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_20_R1.fq.gz to zrtg3644_20_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_20_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_20_R2.fq.gz to zrtg3644_20_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_20_R2.fq.gz to zrtg3644_20_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_20_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_20_R1.fq.gz_C_to_T.fastq and zrtg3644_20_R1.fq.gz_G_to_A.fastq and zrtg3644_20_R2.fq.gz_C_to_T.fastq and zrtg3644_20_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_20_R1.fq.gz_C_to_T.fastq and zrtg3644_20_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2790:1000_1:N:0:NCGTTGGT+GGAAGTAT/1 99 NC_047566.1_CT_converted 30638354 23 42M1D73M = 30638505 265 AAATAATGTTGGTATATATTAATTTGTATTTTTTTTTAATTATTTATAATTTAATTTAAATTATATGAGTGTTTTTTAAATTAGTAAAGTGATTGTATTTGTGTTTAAGGTGATT FFFFFFFF,FF,F:F:FFF:F::FFFF:F,F:FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF,FF:FFF:FFF,FF:FF:,FFFF:FFFFF AS:i:-32 XN:i:0 XM:i:4 XO:i:1 XG:i:1 NM:i:5 MD:Z:27T14^T22T6G37A5 YS:i:-30 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2790:1000_2:N:0:NCGTTGGT+GGAAGTAT/2 147 NC_047566.1_CT_converted 30638505 23 114M = 30638354 -265 GTATGTTTTTAATGATAGAATGTGTATAAAGAGAGGTTATTTTTTTTAATAGAAGTTTTTGTTTTTGAGTTGATGGAATAAATTTTAGATTGTTAAGTTTTGTTTTATTTTTTA :FFFF:FFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-30 XN:i:0 XM:i:5 XO:i:0 XG:i:0 NM:i:5 MD:Z:28T3A46G22G10G0 YS:i:-32 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_20_R1.fq.gz_G_to_A.fastq and zrtg3644_20_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2790:1000_1:N:0:NCGTTGGT+GGAAGTAT/1 77 * 0 0 * * 0 0 AAATAATATTAATATATATTAATTTATATTTTTTTTTAATTATTTATAATTTAATTTAAATTATATAAATATTCTTTAAATTAATAAAATAATTATATTTATATTTAAAATAATT FFFFFFFF,FF,F:F:FFF:F::FFFF:F,F:FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF,FF:FFF:FFF,FF:FF:,FFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2790:1000_2:N:0:NCGTTGGT+GGAAGTAT/2 141 * 0 0 * * 0 0 TAAAAAATAAAATAAAATTTAATAATTTAAAATTTATTTTATTAATTTAAAAATAAAAATTTTTATTAAAAAAAATAATTTTTTTTTATATATATTTTATTATTAAAAATATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_20_R1.fq.gz_G_to_A.fastq and zrtg3644_20_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2790:1000_1:N:0:NCGTTGGT+GGAAGTAT/1 77 * 0 0 * * 0 0 AAATAATATTAATATATATTAATTTATATTTTTTTTTAATTATTTATAATTTAATTTAAATTATATAAATATTCTTTAAATTAATAAAATAATTATATTTATATTTAAAATAATT FFFFFFFF,FF,F:F:FFF:F::FFFF:F,F:FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF,FF:FFF:FFF,FF:FF:,FFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2790:1000_2:N:0:NCGTTGGT+GGAAGTAT/2 141 * 0 0 * * 0 0 TAAAAAATAAAATAAAATTTAATAATTTAAAATTTATTTTATTAATTTAAAAATAAAAATTTTTATTAAAAAAAATAATTTTTTTTTATATATATTTTATTATTAAAAATATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFFF: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_20_R1.fq.gz_C_to_T.fastq and zrtg3644_20_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2790:1000_1:N:0:NCGTTGGT+GGAAGTAT/1 77 * 0 0 * * 0 0 AAATAATGTTGGTATATATTAATTTGTATTTTTTTTTAATTATTTATAATTTAATTTAAATTATATGAGTGTTTTTTAAATTAGTAAAGTGATTGTATTTGTGTTTAAGGTGATT FFFFFFFF,FF,F:F:FFF:F::FFFF:F,F:FFFF:FFFFFFFFFFFFFF::FFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFF,FF:FFF:FFF,FF:FF:,FFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2790:1000_2:N:0:NCGTTGGT+GGAAGTAT/2 141 * 0 0 * * 0 0 TAAAAAATAAAACAAAACTTAACAATCTAAAATTTATTCCATCAACTCAAAAACAAAAACTTCTATTAAAAAAAATAACCTCTCTTTATACACATTCTATCATTAAAAACATAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF:FFFF: YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_20_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:9046:5228_1:N:0:GCGTTGGT+GGAAGTAT NC_001276.1 18113 Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:22516:19664_1:N:0:GCGTTGGT+GGAAGTAT NW_022994957.1 201034 100000 reads; of these: 100000 (100.00%) were paired; of these: 74249 (74.25%) aligned concordantly 0 times 11764 (11.76%) aligned concordantly exactly 1 time 13987 (13.99%) aligned concordantly >1 times 25.75% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72673 (72.67%) aligned concordantly 0 times 12469 (12.47%) aligned concordantly exactly 1 time 14858 (14.86%) aligned concordantly >1 times 27.33% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 74263 (74.26%) aligned concordantly 0 times 11764 (11.76%) aligned concordantly exactly 1 time 13973 (13.97%) aligned concordantly >1 times 25.74% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72618 (72.62%) aligned concordantly 0 times 12436 (12.44%) aligned concordantly exactly 1 time 14946 (14.95%) aligned concordantly >1 times 27.38% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_20_R1.fq.gz_C_to_T.fastq, zrtg3644_20_R1.fq.gz_G_to_A.fastq, zrtg3644_20_R2.fq.gz_C_to_T.fastq and zrtg3644_20_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61434 Mapping efficiency: 61.4% Sequence pairs with no alignments under any condition: 22558 Sequence pairs did not map uniquely: 16008 Sequence pairs which were discarded because genomic sequence could not be extracted: 2 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 14902 ((converted) top strand) GA/CT/CT: 15777 (complementary to (converted) top strand) GA/CT/GA: 15781 (complementary to (converted) bottom strand) CT/GA/GA: 14972 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2172545 Total methylated C's in CpG context: 28306 Total methylated C's in CHG context: 1779 Total methylated C's in CHH context: 7639 Total methylated C's in Unknown context: 81 Total unmethylated C's in CpG context: 253674 Total unmethylated C's in CHG context: 376473 Total unmethylated C's in CHH context: 1504674 Total unmethylated C's in Unknown context: 5214 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_21_R1.fq.gz to zrtg3644_21_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_21_R1.fq.gz to zrtg3644_21_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_21_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_21_R2.fq.gz to zrtg3644_21_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_21_R2.fq.gz to zrtg3644_21_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_21_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_21_R1.fq.gz_C_to_T.fastq and zrtg3644_21_R1.fq.gz_G_to_A.fastq and zrtg3644_21_R2.fq.gz_C_to_T.fastq and zrtg3644_21_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_21_R1.fq.gz_C_to_T.fastq and zrtg3644_21_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1723:1000_1:N:0:NCATATCC+ATTGCACA/1 77 * 0 0 * * 0 0 ATTTTTATATTAAAATAAATATATATTATTTTTTATAAAAAAATTTTTTAAATTTTATAAAATTTATAAATATTAAATAAAATTATTTTTATTAATTTTAAATAAATTATATAT FFF:::FFFFFFFF:FFF:FFFFF:FFFF,:FF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:,FFF,,FFFFFFF,,FFFF:FFF:FFF:F:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1723:1000_2:N:0:NCATATCC+ATTGCACA/2 141 * 0 0 * * 0 0 AAAAAATAAATAATTATATATATAATTTATTTAAAATTAATAAAAATAATTTTATTTAATATTTATAAATTTTATAAAATTTAAAAAATTTTTTTATAAAAAATAATATATATTT FFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,::,FFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFF:F:FFFFF,:FF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_21_R1.fq.gz_G_to_A.fastq and zrtg3644_21_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1723:1000_1:N:0:NCATATCC+ATTGCACA/1 99 NC_047565.1_GA_converted 34399192 12 114M = 34399208 131 ATTCCCACACTAAAACAAATATACACCATCCTTCATAAAAAAATTTTTCAAATTCCATAAAATTTATAAATATTAAATAAAACTATCCCCATTAACCTTAAATAAATTACACAT FFF:::FFFFFFFF:FFF:FFFFF:FFFF,:FF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:,FFF,,FFFFFFF,,FFFF:FFF:FFF:F:FF AS:i:-12 XS:i:-20 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:7A4T101 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1723:1000_2:N:0:NCATATCC+ATTGCACA/2 147 NC_047565.1_GA_converted 34399208 12 115M = 34399192 -131 AAATATACACCATCCTTCATAAAAAAATTTTTCAAATTCCATAAAATTTATAAATATTAAATAAAACTATCCCCATTAACCTTAAATAAATTACACATATAATTATTTATTCTTT FFFFFFFFFF:FF:,FFFFF:F:FFFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFF,::,FFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFF AS:i:0 XS:i:-8 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:115 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_21_R1.fq.gz_G_to_A.fastq and zrtg3644_21_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1723:1000_1:N:0:NCATATCC+ATTGCACA/1 83 NC_047563.1_CT_converted 51129147 7 114M = 51129130 -131 ATGTGTAATTTATTTAAGGTTAATGGGGATAGTTTTATTTAATATTTATAAATTTTATGGAATTTGAAAAATTTTTTTATGAAGGATGGTGTATATTTGTTTTAGTGTGGGAAT FF:F:FFF:FFF:FFFF,,FFFFFFF,,FFF,:FFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FF:,FFFF:FFFFF:FFF:FFFFFFFF:::FFF AS:i:-12 XS:i:-24 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:84A21T7 YS:i:-6 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1723:1000_2:N:0:NCATATCC+ATTGCACA/2 163 NC_047563.1_CT_converted 51129130 7 115M = 51129147 131 AAAGAATAAATAATTATATGTGTAATTTATTTAAGGTTAATGGGGATAGTTTTATTTAATATTTATAAATTTTATGGAATTTGAAAAATTTTTTTATGAAGGATGGTGTATATTT FFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,::,FFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFF:F:FFFFF,:FF:FFFFFFFFFF AS:i:-6 XS:i:-12 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:101A13 YS:i:-12 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_21_R1.fq.gz_C_to_T.fastq and zrtg3644_21_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1723:1000_1:N:0:NCATATCC+ATTGCACA/1 77 * 0 0 * * 0 0 ATTTTTATATTAAAATAAATATATATTATTTTTTATAAAAAAATTTTTTAAATTTTATAAAATTTATAAATATTAAATAAAATTATTTTTATTAATTTTAAATAAATTATATAT FFF:::FFFFFFFF:FFF:FFFFF:FFFF,:FF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFF:,FFF,,FFFFFFF,,FFFF:FFF:FFF:F:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1723:1000_2:N:0:NCATATCC+ATTGCACA/2 141 * 0 0 * * 0 0 AAAAAATAAATAATTATATATATAATTTATTTAAAATTAATAAAAATAATTTTATTTAATATTTATAAATTTTATAAAATTTAAAAAATTTTTTTATAAAAAATAATATATATTT FFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,::,FFFFFFFFFFFFFFF:FFFF:FFFF:FFFFFFFFFFFFFFFF:F:FFFFF,:FF:FFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_21_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73577 (73.58%) aligned concordantly 0 times 11867 (10000011.87 reads; of these:% ) aligned concordantly exactly 1 time 100000 (14556 (14.56100.00%%) aligned concordantly >1 times) were paired; of these: 26.42 %73527 overall alignment rate ( 73.53%) aligned concordantly 0 times 11993 (11.99%) aligned concordantly exactly 1 time 14480 (14.48%) aligned concordantly >1 times 26.47% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73319 (73.32%) aligned concordantly 0 times 12040 (12.04%) aligned concordantly exactly 1 time 14641 (14.64%) aligned concordantly >1 times 26.68% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73417 (73.42%) aligned concordantly 0 times 11955 (11.96%) aligned concordantly exactly 1 time 14628 (14.63%) aligned concordantly >1 times 26.58% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_21_R1.fq.gz_C_to_T.fastq, zrtg3644_21_R1.fq.gz_G_to_A.fastq, zrtg3644_21_R2.fq.gz_C_to_T.fastq and zrtg3644_21_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61032 Mapping efficiency: 61.0% Sequence pairs with no alignments under any condition: 22878 Sequence pairs did not map uniquely: 16090 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15175 ((converted) top strand) GA/CT/CT: 15248 (complementary to (converted) top strand) GA/CT/GA: 15358 (complementary to (converted) bottom strand) CT/GA/GA: 15251 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2159763 Total methylated C's in CpG context: 29050 Total methylated C's in CHG context: 1750 Total methylated C's in CHH context: 7297 Total methylated C's in Unknown context: 71 Total unmethylated C's in CpG context: 250564 Total unmethylated C's in CHG context: 375069 Total unmethylated C's in CHH context: 1496033 Total unmethylated C's in Unknown context: 5010 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_22_R1.fq.gz to zrtg3644_22_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_22_R1.fq.gz to zrtg3644_22_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_22_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_22_R2.fq.gz to zrtg3644_22_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_22_R2.fq.gz to zrtg3644_22_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_22_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_22_R1.fq.gz_C_to_T.fastq and zrtg3644_22_R1.fq.gz_G_to_A.fastq and zrtg3644_22_R2.fq.gz_C_to_T.fastq and zrtg3644_22_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_22_R1.fq.gz_C_to_T.fastq and zrtg3644_22_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2519:1000_1:N:0:NCATAGAT+CACCTTAA/1 77 * 0 0 * * 0 0 TTATATTATTAAATATTAAAAATTAATAAAATTTTAATTAAATTATTAATTTTATTATAAATAAATTAATATTAATAATAATATTAAAAATTTTTTATATTTTATTAATTAATTT FFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFF:F:F:FFFFFFFFFFFF,,FFF:F::,FF:,: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2519:1000_2:N:0:NCATAGAT+CACCTTAA/2 141 * 0 0 * * 0 0 ATTTTAATAATAATTTATATTAAAATTTAATAAAAAAAAATTAATAAATTAAAATTTAAAAATTTAAAATTTAAATTAATTTATATTATTTAAAATTTTTATATAAATAAAAAT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:F::FFFFFFF,:FFFFFFFFFFFFF:FFFFFFF:F:FFFFF:FFFFFF:FFFFFFF,FFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_22_R1.fq.gz_G_to_A.fastq and zrtg3644_22_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2519:1000_1:N:0:NCATAGAT+CACCTTAA/1 99 NC_047568.1_GA_converted 48583968 42 115M = 48584249 395 TTATACCATTAAATATTAAAAATTAATAAAATTCTAATTAAACCATCAATTTTACTATAAACAAATCAATATTAATAATAATATCAAAAATCTCTTATACCCCATTAATCAATTT FFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFF:F:F:FFFFFFFFFFFF,,FFF:F::,FF:,: AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:115 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2519:1000_2:N:0:NCATAGAT+CACCTTAA/2 147 NC_047568.1_GA_converted 48584249 42 114M = 48583968 -395 ACTTTTATCTATATAAAAATTTCAAATAACACAAATCAACCCAAATTTTAAATCCTCAAACCCTAATCTACCAACCTTTTCCTACTAAATTTTAACATAAACTATTATCAAAAT FF:FFFFFFFF,FFFFFFF:FFFFFF:FFFFF:F:FFFFFFF:FFFFFFFFFFFFF:,FFFFFFF::F:FFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFF AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:114 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_22_R1.fq.gz_G_to_A.fastq and zrtg3644_22_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2519:1000_1:N:0:NCATAGAT+CACCTTAA/1 77 * 0 0 * * 0 0 TTATACCATTAAATATTAAAAATTAATAAAATTCTAATTAAACCATCAATTTTACTATAAACAAATCAATATTAATAATAATATCAAAAATCTCTTATACCCCATTAATCAATTT FFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFF:F:F:FFFFFFFFFFFF,,FFF:F::,FF:,: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2519:1000_2:N:0:NCATAGAT+CACCTTAA/2 141 * 0 0 * * 0 0 ATTTTGATAATAGTTTATGTTAAAATTTAGTAGGAAAAGGTTGGTAGATTAGGGTTTGAGGATTTAAAATTTGGGTTGATTTGTGTTATTTGAAATTTTTATATAGATAAAAGT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:F::FFFFFFF,:FFFFFFFFFFFFF:FFFFFFF:F:FFFFF:FFFFFF:FFFFFFF,FFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_22_R1.fq.gz_C_to_T.fastq and zrtg3644_22_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2519:1000_1:N:0:NCATAGAT+CACCTTAA/1 77 * 0 0 * * 0 0 TTATATTATTAAATATTAAAAATTAATAAAATTTTAATTAAATTATTAATTTTATTATAAATAAATTAATATTAATAATAATATTAAAAATTTTTTATATTTTATTAATTAATTT FFFFFF,FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFF,FFFFFFFFFFFFFFFFF:F:FFFFFFFFFFF:FFFF:F:F:FFFFFFFFFFFF,,FFF:F::,FF:,: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2519:1000_2:N:0:NCATAGAT+CACCTTAA/2 141 * 0 0 * * 0 0 ATTTTAATAATAATTTATATTAAAATTTAATAAAAAAAAATTAATAAATTAAAATTTAAAAATTTAAAATTTAAATTAATTTATATTATTTAAAATTTTTATATAAATAAAAAT FFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFF:F::FFFFFFF,:FFFFFFFFFFFFF:FFFFFFF:F:FFFFF:FFFFFF:FFFFFFF,FFFFFFFF:FF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_22_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1101:4309:8860_1:N:0:TCATAGAT+CACCTTAA NW_022994946.1 2 100000 reads; of these: 100000 (100.00%) were paired; of these: 73084 (73.08%) aligned concordantly 0 times 12274 (12.27%) aligned concordantly exactly 1 time 14642 (14.64%) aligned concordantly >1 times 26.92% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73308 (73.31%) aligned concordantly 0 times 12257 (12.26%) aligned concordantly exactly 1 time 14435 (14.44%) aligned concordantly >1 times 26.69% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73572 (73.57%) aligned concordantly 0 times 11979 (11.98%) aligned concordantly exactly 1 time 14449 (14.45%) aligned concordantly >1 times 26.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73066 (73.07%) aligned concordantly 0 times 12103 (12.10%) aligned concordantly exactly 1 time 14831 (14.83%) aligned concordantly >1 times 26.93% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_22_R1.fq.gz_C_to_T.fastq, zrtg3644_22_R1.fq.gz_G_to_A.fastq, zrtg3644_22_R2.fq.gz_C_to_T.fastq and zrtg3644_22_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61649 Mapping efficiency: 61.6% Sequence pairs with no alignments under any condition: 22150 Sequence pairs did not map uniquely: 16201 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15254 ((converted) top strand) GA/CT/CT: 15516 (complementary to (converted) top strand) GA/CT/GA: 15438 (complementary to (converted) bottom strand) CT/GA/GA: 15440 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2190236 Total methylated C's in CpG context: 28825 Total methylated C's in CHG context: 1891 Total methylated C's in CHH context: 7592 Total methylated C's in Unknown context: 55 Total unmethylated C's in CpG context: 257120 Total unmethylated C's in CHG context: 381906 Total unmethylated C's in CHH context: 1512902 Total unmethylated C's in Unknown context: 5309 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.0% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_23_R1.fq.gz to zrtg3644_23_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_23_R1.fq.gz to zrtg3644_23_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_23_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_23_R2.fq.gz to zrtg3644_23_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_23_R2.fq.gz to zrtg3644_23_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_23_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_23_R1.fq.gz_C_to_T.fastq and zrtg3644_23_R1.fq.gz_G_to_A.fastq and zrtg3644_23_R2.fq.gz_C_to_T.fastq and zrtg3644_23_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_23_R1.fq.gz_C_to_T.fastq and zrtg3644_23_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3206:1000_1:N:0:NTATTCCA+TTGTCTAC/1 99 NC_047564.1_CT_converted 52276293 40 33M1I81M = 52276309 127 AGTAGAAATAATTTATGGGGGAGTTAATGATGGAAAAAATGTTTATTGGGTATTTTAGAGATAGTATAGAAATTAATTTAATTAGTTTTAATATATATTGTTTATTAAAAATAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:F:FFFFFF AS:i:-8 XN:i:0 XM:i:0 XO:i:1 XG:i:1 NM:i:1 MD:Z:114 YS:i:-26 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:3206:1000_2:N:0:NTATTCCA+TTGTCTAC/2 147 NC_047564.1_CT_converted 52276309 40 17M1I94M = 52276293 -127 GGGGTAGTTAAAGATGGAAAAAATGTTTATTGGGTATATTAGAGATAGTATAGAAATTAATTTAATTAGTTTTAATATATATTGTTTATTAAAAATAATAGAGATAGTTATT :F,,,F,,,FF,:F,,,FFFFFF,,,:,F,,,,,,:,,:,F:F,F,F,,F:F,FFF::FFF,FFF:FF:,:::FF:FFFFF,F:,F,FF:FFFFFFFFFFFF:F:F:::F:, AS:i:-26 XN:i:0 XM:i:3 XO:i:1 XG:i:1 NM:i:4 MD:Z:4G6T24T74 YS:i:-8 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_23_R1.fq.gz_G_to_A.fastq and zrtg3644_23_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3206:1000_1:N:0:NTATTCCA+TTGTCTAC/1 77 * 0 0 * * 0 0 AATAAAAATAATTTATAAAAAAATTAATAATAAAAAAAATATTTATTAAATATTTTAAAAATAATATAAAAATTAATTTAATTAATTTTAATATATATTATTTATTAAAAATAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:F:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3206:1000_2:N:0:NTATTCCA+TTGTCTAC/2 141 * 0 0 * * 0 0 AATAATTATTTTTATTATTTTTAATAAATAATATATATTAAAATTAATTAAATTAATTTTTATATTATTTTTAATATATTTAATAAATATTTTTTTTATTTTTAATTGTTTT ,:F:::F:F:FFFFFFFFFFFF:FF,F,:F,FFFFF:FF:::,:FF:FFF,FFF::FFF,F:F,,F,F,F:F,:,,:,,,,,,F,:,,,FFFFFF,,,F:,FF,,,F,,,F: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_23_R1.fq.gz_G_to_A.fastq and zrtg3644_23_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3206:1000_1:N:0:NTATTCCA+TTGTCTAC/1 77 * 0 0 * * 0 0 AATAAAAATAATTTATAAAAAAATTAATAATAAAAAAAATATTTATTAAATATTTTAAAAATAATATAAAAATTAATTTAATTAATTTTAATATATATTATTTATTAAAAATAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:F:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3206:1000_2:N:0:NTATTCCA+TTGTCTAC/2 141 * 0 0 * * 0 0 AATAATTATTTTTATTATTTTTAATAAATAATATATATTAAAATTAATTAAATTAATTTTTATATTATTTTTAATATATTTAATAAATATTTTTTTTATTTTTAATTGTTTT ,:F:::F:F:FFFFFFFFFFFF:FF,F,:F,FFFFF:FF:::,:FF:FFF,FFF::FFF,F:F,,F,F,F:F,:,,:,,,,,,F,:,,,FFFFFF,,,F:,FF,,,F,,,F: YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_23_R1.fq.gz_C_to_T.fastq and zrtg3644_23_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:3206:1000_1:N:0:NTATTCCA+TTGTCTAC/1 77 * 0 0 * * 0 0 AGTAGAAATAATTTATGGGGGAGTTAATGATGGAAAAAATGTTTATTGGGTATTTTAGAGATAGTATAGAAATTAATTTAATTAGTTTTAATATATATTGTTTATTAAAAATAAT FFFF:FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF,:FFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFF:F:FFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:3206:1000_2:N:0:NTATTCCA+TTGTCTAC/2 141 * 0 0 * * 0 0 AATAACTATCTCTATTATTTTTAATAAACAATATATATTAAAACTAATTAAATTAATTTCTATACTATCTCTAATATACCCAATAAACATTTTTTCCATCTTTAACTACCCC ,:F:::F:F:FFFFFFFFFFFF:FF,F,:F,FFFFF:FF:::,:FF:FFF,FFF::FFF,F:F,,F,F,F:F,:,,:,,,,,,F,:,,,FFFFFF,,,F:,FF,,,F,,,F: YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_23_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72654 (72.65%) aligned concordantly 0 times 12322 (12.32%) aligned concordantly exactly 1 time 15024 (15.02%) aligned concordantly >1 times 27.35% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73212 (73.21%) aligned concordantly 0 times 11832 (11.83%) aligned concordantly exactly 1 time 14956 (14.96%) aligned concordantly >1 times 26.79% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72926 (72.93%) aligned concordantly 0 times 12138 (12.14%) aligned concordantly exactly 1 time 14936 (14.94%) aligned concordantly >1 times 27.07% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73239 (73.24%) aligned concordantly 0 times 11877 (11.88%) aligned concordantly exactly 1 time 14884 (14.88%) aligned concordantly >1 times 26.76% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_23_R1.fq.gz_C_to_T.fastq, zrtg3644_23_R1.fq.gz_G_to_A.fastq, zrtg3644_23_R2.fq.gz_C_to_T.fastq and zrtg3644_23_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61099 Mapping efficiency: 61.1% Sequence pairs with no alignments under any condition: 21844 Sequence pairs did not map uniquely: 17057 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15266 ((converted) top strand) GA/CT/CT: 15111 (complementary to (converted) top strand) GA/CT/GA: 15014 (complementary to (converted) bottom strand) CT/GA/GA: 15708 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2149766 Total methylated C's in CpG context: 28319 Total methylated C's in CHG context: 1908 Total methylated C's in CHH context: 7403 Total methylated C's in Unknown context: 43 Total unmethylated C's in CpG context: 252710 Total unmethylated C's in CHG context: 375553 Total unmethylated C's in CHH context: 1483873 Total unmethylated C's in Unknown context: 5247 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 0.8% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_24_R1.fq.gz to zrtg3644_24_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_24_R1.fq.gz to zrtg3644_24_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_24_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_24_R2.fq.gz to zrtg3644_24_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_24_R2.fq.gz to zrtg3644_24_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_24_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_24_R1.fq.gz_C_to_T.fastq and zrtg3644_24_R1.fq.gz_G_to_A.fastq and zrtg3644_24_R2.fq.gz_C_to_T.fastq and zrtg3644_24_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_24_R1.fq.gz_C_to_T.fastq and zrtg3644_24_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1163:1000_1:N:0:NCTCCGTC+CACCGATG/1 99 NC_047560.1_CT_converted 24506074 0 112M = 24506106 149 GGGTTTTAGTATAGTTAGTTTAATATATTTTTTTATGTTAATGTGTGGGGTTTTAGTATAGTTAGTTTATTTGTTTTTTTTTAGATTTTAAATTATTTTTTTTTTTATATAT FF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::,:FFFFFFFFFFFFFFFFFFFF AS:i:-36 XS:i:-36 XN:i:0 XM:i:6 XO:i:0 XG:i:0 NM:i:6 MD:Z:28G0A39A34A2A0T3 YS:i:-39 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1163:1000_2:N:0:NCTCCGTC+CACCGATG/2 147 NC_047560.1_CT_converted 24506106 0 72M4D3M1D3M1I34M = 24506074 -149 TTATGTTAATGTGTGGGGTTTTAGTATAGTTAGTTTATTTGTTTTTTTTTAGATTTTAAATTATTTTTTTTTTTATATATTTTTTTTGATAGGTATTGTTTTTTTGATAAAGG FF:FFFFFFFFF::FFF,FFF:F:FFFF,FFF,FFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF AS:i:-39 XS:i:-51 XN:i:0 XM:i:1 XO:i:3 XG:i:6 NM:i:7 MD:Z:37A34^ATAA3^T37 YS:i:-36 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_24_R1.fq.gz_G_to_A.fastq and zrtg3644_24_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1163:1000_1:N:0:NCTCCGTC+CACCGATG/1 77 * 0 0 * * 0 0 AAATTTTAATATAATTAATTTAATATATTTTTTTATATTAATATATAAAATTTTAATATAATTAATTTATTTATTTTTTTTTAAATTTTAAATTATTTTTTTTTTTATATAT FF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::,:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1163:1000_2:N:0:NCTCCGTC+CACCGATG/2 141 * 0 0 * * 0 0 TTTTTATTAAAAAAATAATATTTATTAAAAAAAATATATAAAAAAAAAAATAATTTAAAATTTAAAAAAAAATAAATAAATTAATTATATTAAAATTTTATATATTAATATAA FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFF,FFFF:F:FFF,FFF::FFFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_24_R1.fq.gz_G_to_A.fastq and zrtg3644_24_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1163:1000_1:N:0:NCTCCGTC+CACCGATG/1 77 * 0 0 * * 0 0 AAATTTTAATATAATTAATTTAATATATTTTTTTATATTAATATATAAAATTTTAATATAATTAATTTATTTATTTTTTTTTAAATTTTAAATTATTTTTTTTTTTATATAT FF:FFFFFFFF:FF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::,:FFFFFFFFFFFFFFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1163:1000_2:N:0:NCTCCGTC+CACCGATG/2 141 * 0 0 * * 0 0 TTTTTATTAAAAAAATAATATTTATTAAAAAAAATATATAAAAAAAAAAATAATTTAAAATTTAAAAAAAAATAAATAAATTAATTATATTAAAATTTTATATATTAATATAA FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFF,FFFF:F:FFF,FFF::FFFFFFFFF:FF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_24_R1.fq.gz_C_to_T.fastq and zrtg3644_24_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1163:1000_1:N:0:NCTCCGTC+CACCGATG/1 83 NC_047567.1_GA_converted 20698053 15 112M = 20698018 -147 ATATATAAAAAAAAAAATAATTTAAAATCTAAAAAAAAACAAATAAACTAACTATACTAAAACCCCACACATTAACATAAAAAAATATATTAAACTAACTATACTAAAACCC FFFFFFFFFFFFFFFFFFFF:,::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF:FFFFFFFF:FF AS:i:-12 XS:i:-36 XN:i:0 XM:i:2 XO:i:0 XG:i:0 NM:i:2 MD:Z:42T39T29 YS:i:-17 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1163:1000_2:N:0:NCTCCGTC+CACCGATG/2 163 NC_047567.1_GA_converted 20698018 15 26M2D87M = 20698053 147 CCTTTATCAAAAAAACAATACCTATCAAAAAAAATATATAAAAAAAAAAATAATTTAAAATCTAAAAAAAAACAAATAAACTAACTATACTAAAACCCCACACATTAACATAA FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFF,FFF,FFFF:F:FFF,FFF::FFFFFFFFF:FF AS:i:-17 XS:i:-37 XN:i:0 XM:i:1 XO:i:1 XG:i:2 NM:i:3 MD:Z:26^AA49T37 YS:i:-12 YT:Z:CP >>> Writing bisulfite mapping results to zrtg3644_24_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73171 (73.17%) aligned concordantly 0 times 12049 (12.05%) aligned concordantly exactly 1 time 14780 (14.78%) aligned concordantly >1 times 26.83% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72990 (72.99%) aligned concordantly 0 times 12346 (12.35%) aligned concordantly exactly 1 time 14664 (14.66%) aligned concordantly >1 times 27.01% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72992 (72.99%) aligned concordantly 0 times 12384 (12.38%) aligned concordantly exactly 1 time 14624 (14.62%) aligned concordantly >1 times 27.01% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73345 (73.34%) aligned concordantly 0 times 12117 (12.12%) aligned concordantly exactly 1 time 14538 (14.54%) aligned concordantly >1 times 26.66% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_24_R1.fq.gz_C_to_T.fastq, zrtg3644_24_R1.fq.gz_G_to_A.fastq, zrtg3644_24_R2.fq.gz_C_to_T.fastq and zrtg3644_24_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 62084 Mapping efficiency: 62.1% Sequence pairs with no alignments under any condition: 21776 Sequence pairs did not map uniquely: 16140 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15467 ((converted) top strand) GA/CT/CT: 15609 (complementary to (converted) top strand) GA/CT/GA: 15375 (complementary to (converted) bottom strand) CT/GA/GA: 15633 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2208035 Total methylated C's in CpG context: 29099 Total methylated C's in CHG context: 1864 Total methylated C's in CHH context: 7332 Total methylated C's in Unknown context: 58 Total unmethylated C's in CpG context: 258886 Total unmethylated C's in CHG context: 384718 Total unmethylated C's in CHH context: 1526136 Total unmethylated C's in Unknown context: 5293 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_2_R1.fq.gz to zrtg3644_2_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_2_R1.fq.gz to zrtg3644_2_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_2_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_2_R2.fq.gz to zrtg3644_2_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_2_R2.fq.gz to zrtg3644_2_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_2_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_2_R1.fq.gz_C_to_T.fastq and zrtg3644_2_R1.fq.gz_G_to_A.fastq and zrtg3644_2_R2.fq.gz_C_to_T.fastq and zrtg3644_2_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_2_R1.fq.gz_C_to_T.fastq and zrtg3644_2_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2013:1000_1:N:0:NTCATAAG+CCTTCTAA/1 77 * 0 0 * * 0 0 AATATAAATTAATTTTTTAAAAAAAATTTTATTTTAATTATATTATATAAAATATTATATTTTTATTAAATTAATTTAATTTTTTATTAATTATATAAATTTAATTTTTTTTA FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFF,FFFFFFFFF:FFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2013:1000_2:N:0:NTCATAAG+CCTTCTAA/2 141 * 0 0 * * 0 0 ATATTTAAATTTTTATATTTAATAAAAATTAAATTTTAAAATTATTTAATTAATTTTTAAAAAAAATTAAATTTATATAATTAATAAAAAATTAAATTAATTTAATAAAAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFF:FFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_2_R1.fq.gz_G_to_A.fastq and zrtg3644_2_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2013:1000_1:N:0:NTCATAAG+CCTTCTAA/1 99 NC_047565.1_GA_converted 14478947 2 113M = 14479182 349 AATATAAACCAACCCCTTAAAAAAAATCCCATTTTAACTATATTATACAAAATATCACATTTTCACCAAACTAACTTAACCTCTTACTAACCATATAAACCCAATTCCTTTTA FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFF,FFFFFFFFF:FFFFFFFF AS:i:-18 XS:i:-18 XN:i:0 XM:i:3 XO:i:0 XG:i:0 NM:i:3 MD:Z:74T1A14T21 YS:i:-54 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2013:1000_2:N:0:NTCATAAG+CCTTCTAA/2 147 NC_047565.1_GA_converted 14479182 2 114M = 14478947 -349 ACATTTTCACCAAACTAACTTAACCTCTTACTAACCATATAAACCCAATTCCTTTTAAAAATCAACTAAACAATCCCAAAACCCAATTCTCACTAAATATAAAAATCCAAATAT FFFFFFFFF:FFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:F:FFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-54 XS:i:-48 XN:i:0 XM:i:9 XO:i:0 XG:i:0 NM:i:9 MD:Z:1T5T12A7A6T14T33C2C5C20 YS:i:-18 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_2_R1.fq.gz_G_to_A.fastq and zrtg3644_2_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2013:1000_1:N:0:NTCATAAG+CCTTCTAA/1 83 NC_047568.1_CT_converted 12200911 2 113M = 12200675 -349 TAAAAGGAATTGGGTTTATATGGTTAGTAAGAGGTTAAGTTAGTTTGGTGAAAATGTGATATTTTGTATAATATAGTTAAAATGGGATTTTTTTTAAGGGGTTGGTTTATATT FFFFFFFF:FFFFFFFFF,FFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:106G6 YS:i:-48 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2013:1000_2:N:0:NTCATAAG+CCTTCTAA/2 163 NC_047568.1_CT_converted 12200675 2 114M = 12200911 349 ATATTTGGATTTTTATATTTAGTGAGAATTGGGTTTTGGGATTGTTTAGTTGATTTTTAAAAGGAATTGGGTTTATATGGTTAGTAAGAGGTTAAGTTAGTTTGGTGAAAATGT FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFF:FFFFFFFFF AS:i:-48 XS:i:-58 XN:i:0 XM:i:8 XO:i:0 XG:i:0 NM:i:8 MD:Z:14T11G2G33A2A11A8A5T20 YS:i:-6 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_2_R1.fq.gz_C_to_T.fastq and zrtg3644_2_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2013:1000_1:N:0:NTCATAAG+CCTTCTAA/1 77 * 0 0 * * 0 0 AATATAAATTAATTTTTTAAAAAAAATTTTATTTTAATTATATTATATAAAATATTATATTTTTATTAAATTAATTTAATTTTTTATTAATTATATAAATTTAATTTTTTTTA FFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFF,FFFFFFFFF:FFFFFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2013:1000_2:N:0:NTCATAAG+CCTTCTAA/2 141 * 0 0 * * 0 0 ATATTTAAATTTTTATATTTAATAAAAATTAAATTTTAAAATTATTTAATTAATTTTTAAAAAAAATTAAATTTATATAATTAATAAAAAATTAAATTAATTTAATAAAAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFF:F:FFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFF:FFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_2_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73457 (73.46%) aligned concordantly 0 times 11994 (11.99%) aligned concordantly exactly 1 time 14549 (14.55%) aligned concordantly >1 times 26.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73608 (73.61%) aligned concordantly 0 times 11962 (11.96%) aligned concordantly exactly 1 time 14430 (14.43%) aligned concordantly >1 times 26.39% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73460 (73.46%) aligned concordantly 0 times 12084 (12.08%) aligned concordantly exactly 1 time 14456 (14.46%) aligned concordantly >1 times 26.54% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73697 (73.70%) aligned concordantly 0 times 11896 (11.90%) aligned concordantly exactly 1 time 14407 (14.41%) aligned concordantly >1 times 26.30% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_2_R1.fq.gz_C_to_T.fastq, zrtg3644_2_R1.fq.gz_G_to_A.fastq, zrtg3644_2_R2.fq.gz_C_to_T.fastq and zrtg3644_2_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60791 Mapping efficiency: 60.8% Sequence pairs with no alignments under any condition: 23155 Sequence pairs did not map uniquely: 16054 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15044 ((converted) top strand) GA/CT/CT: 14926 (complementary to (converted) top strand) GA/CT/GA: 15404 (complementary to (converted) bottom strand) CT/GA/GA: 15417 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2172850 Total methylated C's in CpG context: 28420 Total methylated C's in CHG context: 1893 Total methylated C's in CHH context: 7850 Total methylated C's in Unknown context: 81 Total unmethylated C's in CpG context: 252139 Total unmethylated C's in CHG context: 374344 Total unmethylated C's in CHH context: 1508204 Total unmethylated C's in Unknown context: 5353 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.5% Bismark completed in 0d 0h 0m 53s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_3_R1.fq.gz to zrtg3644_3_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_3_R1.fq.gz to zrtg3644_3_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_3_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_3_R2.fq.gz to zrtg3644_3_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_3_R2.fq.gz to zrtg3644_3_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_3_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_3_R1.fq.gz_C_to_T.fastq and zrtg3644_3_R1.fq.gz_G_to_A.fastq and zrtg3644_3_R2.fq.gz_C_to_T.fastq and zrtg3644_3_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_3_R1.fq.gz_C_to_T.fastq and zrtg3644_3_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2121:1000_1:N:0:NTCTGCAG+TACATCCA/1 99 NC_047561.1_CT_converted 49664063 23 52M1D30M1D31M = 49664072 124 TTAAAAATGAAAAGAATGTATGGATTTTGAATAGAATTAGTTTTAGGATTTATTTTTTTTTTTAGTTTTTAAATATTGAGGGGTTTTATTTATGTATGTGAATTAATTTTAAT FFFF,FFF:FFF,F:FFF,FFF::FFF,,,FFFFF:FF,FFFFFF:FFFFF:FFF:FFFFF,FF:::FFF,FFF,FFF,FFFFFFF,,,FF,,F,FF,FF,FFFFF:FFFF,F AS:i:-34 XN:i:0 XM:i:3 XO:i:2 XG:i:2 NM:i:5 MD:Z:52^T30^T0T4T4G20 YS:i:-22 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2121:1000_2:N:0:NTCTGCAG+TACATCCA/2 147 NC_047561.1_CT_converted 49664072 23 43M1D30M1D40M = 49664063 -124 AAAAGAATGTATGGATTTTGAATAGAATTAGTTTTAGGATTTATTTTTTTTTTTAGTTTTTAAATATTGAGGGGTTTTTTTTAGGTATGTGAATTAATTTTAATGAATAAAAA F:,F,,,,,,,FF:F::FF:,:FFFF::F,FF,FFF,:F::F:FF:FFFF:,F:FFFFF:FFF:F,F:F,FFFFFFFFF,FFFFF,FFFFFFFFFFFFFFFFFFF,FFFFFFF AS:i:-22 XN:i:0 XM:i:1 XO:i:2 XG:i:2 NM:i:3 MD:Z:43^T30^T0T39 YS:i:-34 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_3_R1.fq.gz_G_to_A.fastq and zrtg3644_3_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2121:1000_1:N:0:NTCTGCAG+TACATCCA/1 77 * 0 0 * * 0 0 TTAAAAATAAAAAAAATATATAAATTTTAAATAAAATTAATTTTAAAATTTATTTTTTTTTTTAATTTTTAAATATTAAAAAATTTTATTTATATATATAAATTAATTTTAAT FFFF,FFF:FFF,F:FFF,FFF::FFF,,,FFFFF:FF,FFFFFF:FFFFF:FFF:FFFFF,FF:::FFF,FFF,FFF,FFFFFFF,,,FF,,F,FF,FF,FFFFF:FFFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2121:1000_2:N:0:NTCTGCAG+TACATCCA/2 141 * 0 0 * * 0 0 TTTTTATTTATTAAAATTAATTTATATATTTAAAAAAAATTTTTTAATATTTAAAAATTAAAAAAAAAAATAAATTTTAAAATTAATTTTATTTAAAATTTATATATTTTTTT FFFFFFF,FFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFF,F:F,F:FFF:FFFFF:F,:FFFF:FF:F::F:,FFF,FF,F::FFFF:,:FF::F:FF,,,,,,,F,:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_3_R1.fq.gz_G_to_A.fastq and zrtg3644_3_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2121:1000_1:N:0:NTCTGCAG+TACATCCA/1 77 * 0 0 * * 0 0 TTAAAAATAAAAAAAATATATAAATTTTAAATAAAATTAATTTTAAAATTTATTTTTTTTTTTAATTTTTAAATATTAAAAAATTTTATTTATATATATAAATTAATTTTAAT FFFF,FFF:FFF,F:FFF,FFF::FFF,,,FFFFF:FF,FFFFFF:FFFFF:FFF:FFFFF,FF:::FFF,FFF,FFF,FFFFFFF,,,FF,,F,FF,FF,FFFFF:FFFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2121:1000_2:N:0:NTCTGCAG+TACATCCA/2 141 * 0 0 * * 0 0 TTTTTATTTATTAAAATTAATTTATATATTTAAAAAAAATTTTTTAATATTTAAAAATTAAAAAAAAAAATAAATTTTAAAATTAATTTTATTTAAAATTTATATATTTTTTT FFFFFFF,FFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFF,F:F,F:FFF:FFFFF:F,:FFFF:FF:F::F:,FFF,FF,F::FFFF:,:FF::F:FF,,,,,,,F,:F YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_3_R1.fq.gz_C_to_T.fastq and zrtg3644_3_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2121:1000_1:N:0:NTCTGCAG+TACATCCA/1 77 * 0 0 * * 0 0 TTAAAAATGAAAAGAATGTATGGATTTTGAATAGAATTAGTTTTAGGATTTATTTTTTTTTTTAGTTTTTAAATATTGAGGGGTTTTATTTATGTATGTGAATTAATTTTAAT FFFF,FFF:FFF,F:FFF,FFF::FFF,,,FFFFF:FF,FFFFFF:FFFFF:FFF:FFFFF,FF:::FFF,FFF,FFF,FFFFFFF,,,FF,,F,FF,FF,FFFFF:FFFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2121:1000_2:N:0:NTCTGCAG+TACATCCA/2 141 * 0 0 * * 0 0 TTTTTATTCATTAAAATTAATTCACATACCTAAAAAAAACCCCTCAATATTTAAAAACTAAAAAAAAAAATAAATCCTAAAACTAATTCTATTCAAAATCCATACATTCTTTT FFFFFFF,FFFFFFFFFFFFFFFFFFF,FFFFF,FFFFFFFFF,F:F,F:FFF:FFFFF:F,:FFFF:FF:F::F:,FFF,FF,F::FFFF:,:FF::F:FF,,,,,,,F,:F YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_3_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73508 (73.51%) aligned concordantly 0 times 11817 (11.82%) aligned concordantly exactly 1 time 14675 (14.68%) aligned concordantly >1 times 26.49% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73041 (73.04%) aligned concordantly 0 times 12084 (12.08%) aligned concordantly exactly 1 time 14875 (14.88%) aligned concordantly >1 times 26.96% overall alignment rate 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (73115 (73.11%) aligned concordantly 0 times100.00 % ) were paired; of these:11961 ( 11.9673297% () aligned concordantly exactly 1 time73.30 % ) aligned concordantly 0 times14924 ( 14.9211933% () aligned concordantly >1 times11.93 %26.89) aligned concordantly exactly 1 time% overall alignment rate 14770 (14.77%) aligned concordantly >1 times 26.70% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_3_R1.fq.gz_C_to_T.fastq, zrtg3644_3_R1.fq.gz_G_to_A.fastq, zrtg3644_3_R2.fq.gz_C_to_T.fastq and zrtg3644_3_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60870 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 22616 Sequence pairs did not map uniquely: 16514 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15284 ((converted) top strand) GA/CT/CT: 15322 (complementary to (converted) top strand) GA/CT/GA: 15195 (complementary to (converted) bottom strand) CT/GA/GA: 15069 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2151592 Total methylated C's in CpG context: 28625 Total methylated C's in CHG context: 1778 Total methylated C's in CHH context: 7188 Total methylated C's in Unknown context: 63 Total unmethylated C's in CpG context: 250192 Total unmethylated C's in CHG context: 372662 Total unmethylated C's in CHH context: 1491147 Total unmethylated C's in Unknown context: 5347 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.2% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_4_R1.fq.gz to zrtg3644_4_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_4_R1.fq.gz to zrtg3644_4_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_4_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_4_R2.fq.gz to zrtg3644_4_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_4_R2.fq.gz to zrtg3644_4_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_4_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_4_R1.fq.gz_C_to_T.fastq and zrtg3644_4_R1.fq.gz_G_to_A.fastq and zrtg3644_4_R2.fq.gz_C_to_T.fastq and zrtg3644_4_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_4_R1.fq.gz_C_to_T.fastq and zrtg3644_4_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1868:1000_1:N:0:NTGACTCT+TGACGGCC/1 99 NC_047565.1_CT_converted 53337481 1 88M = 53337466 -103 TTTGAGGTAAATAAAGAGGTGATATTAGTAGTAAATTGTATGAAGAATTTAATGGTATTAATTGTTTTTATAGAATTTGTGTATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1868:1000_2:N:0:NTGACTCT+TGACGGCC/2 147 NC_047565.1_CT_converted 53337466 1 88M = 53337481 103 GTGTTTTGGAGAAAGTTTGAGGTAAATAAAGAGGTGATATTAGTAGTAAATTGTATGAAGAATTTAATGGTATTAATTGTTTTTATAG FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_4_R1.fq.gz_G_to_A.fastq and zrtg3644_4_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1868:1000_1:N:0:NTGACTCT+TGACGGCC/1 77 * 0 0 * * 0 0 TTTAAAATAAATAAAAAAATAATATTAATAATAAATTATATAAAAAATTTAATAATATTAATTATTTTTATAAAATTTATATATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1868:1000_2:N:0:NTGACTCT+TGACGGCC/2 141 * 0 0 * * 0 0 TTATAAAAATAATTAATATTATTAAATTTTTTATATAATTTATTATTAATATTATTTTTTTATTTATTTTAAATTTTTTTTAAAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_4_R1.fq.gz_G_to_A.fastq and zrtg3644_4_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1868:1000_1:N:0:NTGACTCT+TGACGGCC/1 77 * 0 0 * * 0 0 TTTAAAATAAATAAAAAAATAATATTAATAATAAATTATATAAAAAATTTAATAATATTAATTATTTTTATAAAATTTATATATAAAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,F YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1868:1000_2:N:0:NTGACTCT+TGACGGCC/2 141 * 0 0 * * 0 0 TTATAAAAATAATTAATATTATTAAATTTTTTATATAATTTATTATTAATATTATTTTTTTATTTATTTTAAATTTTTTTTAAAATAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_4_R1.fq.gz_C_to_T.fastq and zrtg3644_4_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1868:1000_1:N:0:NTGACTCT+TGACGGCC/1 83 NC_047562.1_GA_converted 5038900 1 88M = 5038915 103 ATTTATACACAAATTCTATAAAAACAATTAATACCATTAAATTCTTCATACAATTTACTACTAATATCACCTCTTTATTTACCTCAAA F,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1868:1000_2:N:0:NTGACTCT+TGACGGCC/2 163 NC_047562.1_GA_converted 5038915 1 88M = 5038900 -103 CTATAAAAACAATTAATACCATTAAATTCTTCATACAATTTACTACTAATATCACCTCTTTATTTACCTCAAACTTTCTCCAAAACAC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:::FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:88 YS:i:0 YT:Z:CP >>> Writing bisulfite mapping results to zrtg3644_4_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73477 (73.48%) aligned concordantly 0 times 11941 (11.94%) aligned concordantly exactly 1 time 14582 (14.58%) aligned concordantly >1 times 26.52% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73204 (73.20%) aligned concordantly 0 times 11848 (11.85%) aligned concordantly exactly 1 time 14948 (14.95%) aligned concordantly >1 times 26.80% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73065 (73.06%) aligned concordantly 0 times 11931 (11.93%) aligned concordantly exactly 1 time 15004 (15.00%) aligned concordantly >1 times 26.93% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73414 (73.41%) aligned concordantly 0 times 11889 (11.89%) aligned concordantly exactly 1 time 14697 (14.70%) aligned concordantly >1 times 26.59% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_4_R1.fq.gz_C_to_T.fastq, zrtg3644_4_R1.fq.gz_G_to_A.fastq, zrtg3644_4_R2.fq.gz_C_to_T.fastq and zrtg3644_4_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61001 Mapping efficiency: 61.0% Sequence pairs with no alignments under any condition: 22625 Sequence pairs did not map uniquely: 16374 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15211 ((converted) top strand) GA/CT/CT: 15263 (complementary to (converted) top strand) GA/CT/GA: 15204 (complementary to (converted) bottom strand) CT/GA/GA: 15323 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2155823 Total methylated C's in CpG context: 28443 Total methylated C's in CHG context: 1706 Total methylated C's in CHH context: 6933 Total methylated C's in Unknown context: 89 Total unmethylated C's in CpG context: 247462 Total unmethylated C's in CHG context: 369756 Total unmethylated C's in CHH context: 1501523 Total unmethylated C's in Unknown context: 5203 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.7% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_5_R1.fq.gz to zrtg3644_5_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_5_R1.fq.gz to zrtg3644_5_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_5_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_5_R2.fq.gz to zrtg3644_5_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_5_R2.fq.gz to zrtg3644_5_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_5_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_5_R1.fq.gz_C_to_T.fastq and zrtg3644_5_R1.fq.gz_G_to_A.fastq and zrtg3644_5_R2.fq.gz_C_to_T.fastq and zrtg3644_5_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_5_R1.fq.gz_C_to_T.fastq and zrtg3644_5_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5267:1000_1:N:0:NCTGGTAT+GTAAGCAA/1 77 * 0 0 * * 0 0 TTAAATATATTTTTATTAATTAAAAAAAATAATAATAATATTTATTTAAATTAATTTTATTAAAATATATTAAATATATTAATATAAATTATATTAAAATTAAATTTTAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5267:1000_2:N:0:NCTGGTAT+GTAAGCAA/2 141 * 0 0 * * 0 0 TATATTATAAAATAATATATATATAAAATAAATTAATTTATTTAATTTTAAATTTAAATTTTATATAAATTAATATTTTTAAATTATATAATATATTATATTTTTTAATTTTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_5_R1.fq.gz_G_to_A.fastq and zrtg3644_5_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5267:1000_1:N:0:NCTGGTAT+GTAAGCAA/1 77 * 0 0 * * 0 0 CTAAACACATCTCTATTAATCAAAAAAAATAATAATAATATCTATTTAAATTAATTTCACCAAAACATACTAAATACACCAATACAAATTACATCAAAATCAAATTTCAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5267:1000_2:N:0:NCTGGTAT+GTAAGCAA/2 141 * 0 0 * * 0 0 TATGTTATAAAATGATGTGTGTGTGAGATGAATTAATTTGTTTGATTTTAGATTTAAATTTTGTATAAATTAATATTTTTAAATTATATAATATGTTATATTTTTTGATTTTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_5_R1.fq.gz_G_to_A.fastq and zrtg3644_5_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5267:1000_1:N:0:NCTGGTAT+GTAAGCAA/1 77 * 0 0 * * 0 0 CTAAACACATCTCTATTAATCAAAAAAAATAATAATAATATCTATTTAAATTAATTTCACCAAAACATACTAAATACACCAATACAAATTACATCAAAATCAAATTTCAATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5267:1000_2:N:0:NCTGGTAT+GTAAGCAA/2 141 * 0 0 * * 0 0 TATGTTATAAAATGATGTGTGTGTGAGATGAATTAATTTGTTTGATTTTAGATTTAAATTTTGTATAAATTAATATTTTTAAATTATATAATATGTTATATTTTTTGATTTTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_5_R1.fq.gz_C_to_T.fastq and zrtg3644_5_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:5267:1000_1:N:0:NCTGGTAT+GTAAGCAA/1 77 * 0 0 * * 0 0 TTAAATATATTTTTATTAATTAAAAAAAATAATAATAATATTTATTTAAATTAATTTTATTAAAATATATTAAATATATTAATATAAATTATATTAAAATTAAATTTTAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:5267:1000_2:N:0:NCTGGTAT+GTAAGCAA/2 141 * 0 0 * * 0 0 TATATTATAAAATAATATATATATAAAATAAATTAATTTATTTAATTTTAAATTTAAATTTTATATAAATTAATATTTTTAAATTATATAATATATTATATTTTTTAATTTTAT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_5_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73439 (73.44%) aligned concordantly 0 times 11885 (11.88%) aligned concordantly exactly 1 time 14676 (14.68%) aligned concordantly >1 times 26.56% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73431 (73.43%) aligned concordantly 0 times 11939 (11.94%) aligned concordantly exactly 1 time 14630 (14.63%) aligned concordantly >1 times 26.57% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73064 (73.06%) aligned concordantly 0 times 12160 (12.16%) aligned concordantly exactly 1 time 14776 (14.78%) aligned concordantly >1 times 26.94% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73201 (73.20%) aligned concordantly 0 times 11946 (11.95%) aligned concordantly exactly 1 time 14853 (14.85%) aligned concordantly >1 times 26.80% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_5_R1.fq.gz_C_to_T.fastq, zrtg3644_5_R1.fq.gz_G_to_A.fastq, zrtg3644_5_R2.fq.gz_C_to_T.fastq and zrtg3644_5_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61139 Mapping efficiency: 61.1% Sequence pairs with no alignments under any condition: 22559 Sequence pairs did not map uniquely: 16302 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15216 ((converted) top strand) GA/CT/CT: 15406 (complementary to (converted) top strand) GA/CT/GA: 15321 (complementary to (converted) bottom strand) CT/GA/GA: 15196 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2170069 Total methylated C's in CpG context: 28450 Total methylated C's in CHG context: 1869 Total methylated C's in CHH context: 7456 Total methylated C's in Unknown context: 74 Total unmethylated C's in CpG context: 249726 Total unmethylated C's in CHG context: 375412 Total unmethylated C's in CHH context: 1507156 Total unmethylated C's in Unknown context: 5335 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 50s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_6_R1.fq.gz to zrtg3644_6_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_6_R1.fq.gz to zrtg3644_6_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_6_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_6_R2.fq.gz to zrtg3644_6_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_6_R2.fq.gz to zrtg3644_6_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_6_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_6_R1.fq.gz_C_to_T.fastq and zrtg3644_6_R1.fq.gz_G_to_A.fastq and zrtg3644_6_R2.fq.gz_C_to_T.fastq and zrtg3644_6_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_6_R1.fq.gz_C_to_T.fastq and zrtg3644_6_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1832:1000_1:N:0:NATTAGTG+TATGTAGT/1 77 * 0 0 * * 0 0 TAAAATTAAATATTTATATAAAATATATTTAAAAATAAAATTAATTAATTTAAAATTAATATTATAAATTATAATTTTTTATTATAAAAAATAATATAATTTTTAAATTATTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:F:F:F,,F:FFF,FF:FFF::::,,FF:F,FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1832:1000_2:N:0:NATTAGTG+TATGTAGT/2 141 * 0 0 * * 0 0 TAATTTTTAATTTAAAAATATTTAAAAAAATAATTTAAAAATTATATTATTTTTTATAATAAAAAATTATAATTTATAATATTAATTTTAAATTAATTAATTTTATTTTTAAAT FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_6_R1.fq.gz_G_to_A.fastq and zrtg3644_6_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1832:1000_1:N:0:NATTAGTG+TATGTAGT/1 99 NC_047567.1_GA_converted 36785756 0 58M14D57M = 36785782 154 TAAAATCAAATATTTATACAAAATATATTTAAAAATAAAATTAATCAATCCAAAACTAACACCATAAATTACAATTTTTTACTATAAAAAACAATATAACTCCCAAATCACCCTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:F:F:F,,F:FFF,FF:FFF::::,,FF:F,FFF AS:i:-65 XN:i:0 XM:i:3 XO:i:1 XG:i:14 NM:i:17 MD:Z:58^ACACACTTTTTTAT31T3T16T4 YS:i:-65 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:1832:1000_2:N:0:NATTAGTG+TATGTAGT/2 147 NC_047567.1_GA_converted 36785782 0 32M14D82M = 36785756 -154 ATTTAAAAATAAAATTAATCAATCCAAAACTAACACCATAAATTACAATTTTTTACTATAAAAAACAATATAACTCCCAAATCACCCTTCCAAATATTTTCAAACCAAAAACCA FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFFFF AS:i:-65 XN:i:0 XM:i:3 XO:i:1 XG:i:14 NM:i:17 MD:Z:32^ACACACTTTTTTAT31T3T16T29 YS:i:-65 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_6_R1.fq.gz_G_to_A.fastq and zrtg3644_6_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1832:1000_1:N:0:NATTAGTG+TATGTAGT/1 77 * 0 0 * * 0 0 TAAAATCAAATATTTATACAAAATATATTTAAAAATAAAATTAATCAATCCAAAACTAACACCATAAATTACAATTTTTTACTATAAAAAACAATATAACTCCCAAATCACCCTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:F:F:F,,F:FFF,FF:FFF::::,,FF:F,FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1832:1000_2:N:0:NATTAGTG+TATGTAGT/2 141 * 0 0 * * 0 0 TGGTTTTTGGTTTGAAAATATTTGGAAGGGTGATTTGGGAGTTATATTGTTTTTTATAGTAAAAAATTGTAATTTATGGTGTTAGTTTTGGATTGATTAATTTTATTTTTAAAT FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_6_R1.fq.gz_C_to_T.fastq and zrtg3644_6_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:1832:1000_1:N:0:NATTAGTG+TATGTAGT/1 77 * 0 0 * * 0 0 TAAAATTAAATATTTATATAAAATATATTTAAAAATAAAATTAATTAATTTAAAATTAATATTATAAATTATAATTTTTTATTATAAAAAATAATATAATTTTTAAATTATTTTT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFF:FFFFFFFFFFFFFFFFFFFFFFF:F:F:F,,F:FFF,FF:FFF::::,,FF:F,FFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:1832:1000_2:N:0:NATTAGTG+TATGTAGT/2 141 * 0 0 * * 0 0 TAATTTTTAATTTAAAAATATTTAAAAAAATAATTTAAAAATTATATTATTTTTTATAATAAAAAATTATAATTTATAATATTAATTTTAAATTAATTAATTTTATTTTTAAAT FFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFF:FFFFFFFFFF:FFFFFFFFF:FFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_6_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73064 (73.06%) aligned concordantly 0 times 12228 (12.23%) aligned concordantly exactly 1 time 14708 (14.71%) aligned concordantly >1 times 26.94% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73160 (73.16%) aligned concordantly 0 times 12041 (12.04%) aligned concordantly exactly 1 time 14799 (14.80%) aligned concordantly >1 times 26.84% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73348 (73.35%) aligned concordantly 0 times 11996 (12.00%) aligned concordantly exactly 1 time 14656 (14.66%) aligned concordantly >1 times 26.65% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73351 (73.35%) aligned concordantly 0 times 12135 (12.13%) aligned concordantly exactly 1 time 14514 (14.51%) aligned concordantly >1 times 26.65% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_6_R1.fq.gz_C_to_T.fastq, zrtg3644_6_R1.fq.gz_G_to_A.fastq, zrtg3644_6_R2.fq.gz_C_to_T.fastq and zrtg3644_6_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 61547 Mapping efficiency: 61.5% Sequence pairs with no alignments under any condition: 22163 Sequence pairs did not map uniquely: 16290 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15381 ((converted) top strand) GA/CT/CT: 15556 (complementary to (converted) top strand) GA/CT/GA: 15289 (complementary to (converted) bottom strand) CT/GA/GA: 15321 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2173592 Total methylated C's in CpG context: 28924 Total methylated C's in CHG context: 1803 Total methylated C's in CHH context: 7453 Total methylated C's in Unknown context: 55 Total unmethylated C's in CpG context: 250847 Total unmethylated C's in CHG context: 374871 Total unmethylated C's in CHH context: 1509694 Total unmethylated C's in Unknown context: 5258 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.0% Bismark completed in 0d 0h 0m 52s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_7_R1.fq.gz to zrtg3644_7_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_7_R1.fq.gz to zrtg3644_7_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_7_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_7_R2.fq.gz to zrtg3644_7_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_7_R2.fq.gz to zrtg3644_7_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_7_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_7_R1.fq.gz_C_to_T.fastq and zrtg3644_7_R1.fq.gz_G_to_A.fastq and zrtg3644_7_R2.fq.gz_C_to_T.fastq and zrtg3644_7_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_7_R1.fq.gz_C_to_T.fastq and zrtg3644_7_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2700:1000_1:N:0:NCGGTCAG+AACGAGGC/1 99 NC_047560.1_CT_converted 9052133 18 115M = 9052159 140 TTGTTGAAATTTAATTTTTTGAAAAAAATTTGATATTTTTTTAATTGGTTTGGATGGTGAAAATATGATTTTAGTTTGAAATATATGAAATTTATGTTTAAATATTTTAGTAATT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF:FFFFFFF:FFFFF AS:i:0 XS:i:-24 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:115 YS:i:-6 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2700:1000_2:N:0:NCGGTCAG+AACGAGGC/2 147 NC_047560.1_CT_converted 9052159 18 114M = 9052133 -140 AATTTGATATTTTTTTAATTGGTTTGGATGGTGAAAATATGATTTTAGTTTGAAATATATGAAATTTATGTTTAAATATTTTAGTAATTGTTATAGGATTGTTTTTTAGTATTT FFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-6 XS:i:-30 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:108A5 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_7_R1.fq.gz_G_to_A.fastq and zrtg3644_7_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2700:1000_1:N:0:NCGGTCAG+AACGAGGC/1 77 * 0 0 * * 0 0 TTATTAAAATTTAATTTTTTAAAAAAAATTTAATATTTTTTTAATTAATTTAAATAATAAAAATATAATTTTAATTTAAAATATATAAAATTTATATTTAAATATTTTAATAATT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF:FFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2700:1000_2:N:0:NCGGTCAG+AACGAGGC/2 141 * 0 0 * * 0 0 AAATATTAAAAAATAATTTTATAATAATTATTAAAATATTTAAATATAAATTTTATATATTTTAAATTAAAATTATATTTTTATTATTTAAATTAATTAAAAAAATATTAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_7_R1.fq.gz_G_to_A.fastq and zrtg3644_7_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2700:1000_1:N:0:NCGGTCAG+AACGAGGC/1 77 * 0 0 * * 0 0 TTATTAAAATTTAATTTTTTAAAAAAAATTTAATATTTTTTTAATTAATTTAAATAATAAAAATATAATTTTAATTTAAAATATATAAAATTTATATTTAAATATTTTAATAATT FFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFF:FFFFFFF:FFFFF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2700:1000_2:N:0:NCGGTCAG+AACGAGGC/2 141 * 0 0 * * 0 0 AAATATTAAAAAATAATTTTATAATAATTATTAAAATATTTAAATATAAATTTTATATATTTTAAATTAAAATTATATTTTTATTATTTAAATTAATTAAAAAAATATTAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_7_R1.fq.gz_C_to_T.fastq and zrtg3644_7_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2700:1000_1:N:0:NCGGTCAG+AACGAGGC/1 83 NC_047563.1_GA_converted 58870282 0 115M = 58870257 -140 AATTACTAAAATATTTAAACATAAATTTCATATATTTCAAACTAAAATCATATTTTCACCATCCAAACCAATTAAAAAAATATCAAATTTTTTTCAAAAAATTAAATTTCAACAA FFFFF:FFFFFFF:FFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFF AS:i:-60 XS:i:-60 XN:i:0 XM:i:10 XO:i:0 XG:i:0 NM:i:10 MD:Z:0C5A23C2T8A5A2T11A29C8C12 YS:i:-60 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2700:1000_2:N:0:NCGGTCAG+AACGAGGC/2 163 NC_047563.1_GA_converted 58870257 0 114M = 58870282 140 AAATACTAAAAAACAATCCTATAACAATTACTAAAATATTTAAACATAAATTTCATATATTTCAAACTAAAATCATATTTTCACCATCCAAACCAATTAAAAAAATATCAAATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFF AS:i:-60 XS:i:-60 XN:i:0 XM:i:10 XO:i:0 XG:i:0 NM:i:10 MD:Z:19C2T2C5A23C2T8A5A2T11A25 YS:i:-60 YT:Z:CP >>> Writing bisulfite mapping results to zrtg3644_7_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 73566 (73.57%) aligned concordantly 0 times 11912 (11.91%) aligned concordantly exactly 1 time 14522 (14.52%) aligned concordantly >1 times 26.43% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73811 (73.81%) aligned concordantly 0 times 11664 (11.66%) aligned concordantly exactly 1 time 14525 (14.53%) aligned concordantly >1 times 26.19% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73616 (73.62%) aligned concordantly 0 times 11817 (11.82%) aligned concordantly exactly 1 time 14567 (14.57%) aligned concordantly >1 times 26.38% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73579 (73.58%) aligned concordantly 0 times 11860 (11.86%) aligned concordantly exactly 1 time 14561 (14.56%) aligned concordantly >1 times 26.42% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_7_R1.fq.gz_C_to_T.fastq, zrtg3644_7_R1.fq.gz_G_to_A.fastq, zrtg3644_7_R2.fq.gz_C_to_T.fastq and zrtg3644_7_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60320 Mapping efficiency: 60.3% Sequence pairs with no alignments under any condition: 23556 Sequence pairs did not map uniquely: 16124 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15104 ((converted) top strand) GA/CT/CT: 14956 (complementary to (converted) top strand) GA/CT/GA: 15142 (complementary to (converted) bottom strand) CT/GA/GA: 15118 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2133451 Total methylated C's in CpG context: 28548 Total methylated C's in CHG context: 1785 Total methylated C's in CHH context: 7249 Total methylated C's in Unknown context: 57 Total unmethylated C's in CpG context: 245609 Total unmethylated C's in CHG context: 367100 Total unmethylated C's in CHH context: 1483160 Total unmethylated C's in Unknown context: 5320 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.1% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_8_R1.fq.gz to zrtg3644_8_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_8_R1.fq.gz to zrtg3644_8_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_8_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_8_R2.fq.gz to zrtg3644_8_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_8_R2.fq.gz to zrtg3644_8_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_8_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_8_R1.fq.gz_C_to_T.fastq and zrtg3644_8_R1.fq.gz_G_to_A.fastq and zrtg3644_8_R2.fq.gz_C_to_T.fastq and zrtg3644_8_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_8_R1.fq.gz_C_to_T.fastq and zrtg3644_8_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2899:1000_1:N:0:NGCAAGCC+CGGATGCT/1 77 * 0 0 * * 0 0 TTAATTAAATATATTAAAATAAATTTTAAATTTAAAAATAATATTAATTATATATTATATATATTAATATTATTTTTATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2899:1000_2:N:0:NGCAAGCC+CGGATGCT/2 141 * 0 0 * * 0 0 ATTAATATATATAATATATAATTAATATTATTTTTAAATTTAAAATTTATTTTAATATATTTAATTAAAAATAATTAAATAAT ,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_8_R1.fq.gz_G_to_A.fastq and zrtg3644_8_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2899:1000_1:N:0:NGCAAGCC+CGGATGCT/1 99 NC_047564.1_GA_converted 28353577 39 83M = 28353562 -98 TTAATCAAATATACTAAAATAAACTTTAAATCTAAAAATAACATTAACTATATATCATATACATCAATATTATTTTTATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF: AS:i:0 XS:i:-46 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:83 YS:i:0 YT:Z:CP A00742:173:HMGVGDSXY:2:1101:2899:1000_2:N:0:NGCAAGCC+CGGATGCT/2 147 NC_047564.1_GA_converted 28353562 39 83M = 28353577 98 ATCACTCAATTATTTTTAATCAAATATACTAAAATAAACTTTAAATCTAAAAATAACATTAACTATATATCATATACATCAAT FFFFFF:FFFFFFFFF:FFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFF, AS:i:0 XS:i:-46 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:83 YS:i:0 YT:Z:CP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_8_R1.fq.gz_G_to_A.fastq and zrtg3644_8_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2899:1000_1:N:0:NGCAAGCC+CGGATGCT/1 77 * 0 0 * * 0 0 TTAATCAAATATACTAAAATAAACTTTAAATCTAAAAATAACATTAACTATATATCATATACATCAATATTATTTTTATTATC FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2899:1000_2:N:0:NGCAAGCC+CGGATGCT/2 141 * 0 0 * * 0 0 ATTGATGTATATGATATATAGTTAATGTTATTTTTAGATTTAAAGTTTATTTTAGTATATTTGATTAAAAATAATTGAGTGAT ,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_8_R1.fq.gz_C_to_T.fastq and zrtg3644_8_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:2899:1000_1:N:0:NGCAAGCC+CGGATGCT/1 77 * 0 0 * * 0 0 TTAATTAAATATATTAAAATAAATTTTAAATTTAAAAATAATATTAATTATATATTATATATATTAATATTATTTTTATTATT FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFF: YT:Z:UP A00742:173:HMGVGDSXY:2:1101:2899:1000_2:N:0:NGCAAGCC+CGGATGCT/2 141 * 0 0 * * 0 0 ATTAATATATATAATATATAATTAATATTATTTTTAAATTTAAAATTTATTTTAATATATTTAATTAAAAATAATTAAATAAT ,FFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFF:FFFFFFFFF:FFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_8_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R2.fq.gz Chromosomal sequence could not be extracted for A00742:173:HMGVGDSXY:2:1102:23665:4272_1:N:0:GGCAAGCC+CGGATGCT NW_022994997.1 297113 100000 reads; of these: 100000 (100.00%) were paired; of these: 73061 (73.06%) aligned concordantly 0 times 11911 (11.91%) aligned concordantly exactly 1 time 15028 (15.03%) aligned concordantly >1 times 26.94% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73067 (73.07%) aligned concordantly 0 times 11727 (11.73%) aligned concordantly exactly 1 time 15206 (15.21%) aligned concordantly >1 times 26.93% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73305 (73.31%) aligned concordantly 0 times 11717 (11.72%) aligned concordantly exactly 1 time 14978 (14.98%) aligned concordantly >1 times 26.70% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 73028 (73.03%) aligned concordantly 0 times 11942 (11.94%) aligned concordantly exactly 1 time 15030 (15.03%) aligned concordantly >1 times 26.97% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_8_R1.fq.gz_C_to_T.fastq, zrtg3644_8_R1.fq.gz_G_to_A.fastq, zrtg3644_8_R2.fq.gz_C_to_T.fastq and zrtg3644_8_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60858 Mapping efficiency: 60.9% Sequence pairs with no alignments under any condition: 22549 Sequence pairs did not map uniquely: 16593 Sequence pairs which were discarded because genomic sequence could not be extracted: 1 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15316 ((converted) top strand) GA/CT/CT: 15202 (complementary to (converted) top strand) GA/CT/GA: 15237 (complementary to (converted) bottom strand) CT/GA/GA: 15102 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2144468 Total methylated C's in CpG context: 29213 Total methylated C's in CHG context: 1771 Total methylated C's in CHH context: 7827 Total methylated C's in Unknown context: 73 Total unmethylated C's in CpG context: 248391 Total unmethylated C's in CHG context: 372784 Total unmethylated C's in CHH context: 1484482 Total unmethylated C's in Unknown context: 5270 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.4% Bismark completed in 0d 0h 0m 49s ==================== Bismark run complete ==================== Bowtie 2 seems to be working fine (tested command '/gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/bowtie2 --version' [2.3.4]) Output format is BAM (default) Alignments will be written out in BAM format. Samtools found here: '/gscratch/srlab/programs/samtools-1.4/bin/samtools' Reference genome folder provided is /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ (absolute path is '/gscratch/srlab/sr320/data/Cgig-genome/roslin_M/)' FastQ format assumed (by default) Processing sequences up to read no. 100000 from the input file Each Bowtie 2 instance is going to be run with 4 threads. Please monitor performance closely and tune down if necessary! Input files to be analysed (in current folder '/gscratch/scrubbed/sr320/060921-bigC'): /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R1.fq.gz /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R2.fq.gz Library was specified to be not strand-specific (non-directional), therefore alignments to all four possible bisulfite strands (OT, CTOT, OB and CTOB) will be reported Setting parallelization to single-threaded (default) Summary of all aligner options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Current working directory is: /gscratch/scrubbed/sr320/060921-bigC Now reading in and storing sequence information of the genome specified in: /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ chr NC_047559.1 (55785328 bp) chr NC_047560.1 (73222313 bp) chr NC_047561.1 (58319100 bp) chr NC_047562.1 (53127865 bp) chr NC_047563.1 (73550375 bp) chr NC_047564.1 (60151564 bp) chr NC_047565.1 (62107823 bp) chr NC_047566.1 (58462999 bp) chr NC_047567.1 (37089910 bp) chr NC_047568.1 (57541580 bp) chr NW_022994773.1 (129571 bp) chr NW_022994774.1 (1185781 bp) chr NW_022994775.1 (128451 bp) chr NW_022994776.1 (124569 bp) chr NW_022994777.1 (123505 bp) chr NW_022994778.1 (761972 bp) chr NW_022994779.1 (111600 bp) chr NW_022994780.1 (109880 bp) chr NW_022994781.1 (109004 bp) chr NW_022994782.1 (105193 bp) chr NW_022994783.1 (103107 bp) chr NW_022994784.1 (1334230 bp) chr NW_022994785.1 (99559 bp) chr NW_022994786.1 (93417 bp) chr NW_022994787.1 (85616 bp) chr NW_022994788.1 (84435 bp) chr NW_022994789.1 (725421 bp) chr NW_022994790.1 (78344 bp) chr NW_022994791.1 (77172 bp) chr NW_022994792.1 (66789 bp) chr NW_022994793.1 (66084 bp) chr NW_022994794.1 (699037 bp) chr NW_022994795.1 (63125 bp) chr NW_022994796.1 (62774 bp) chr NW_022994797.1 (60186 bp) chr NW_022994798.1 (59881 bp) chr NW_022994799.1 (680695 bp) chr NW_022994800.1 (57426 bp) chr NW_022994801.1 (56398 bp) chr NW_022994802.1 (52255 bp) chr NW_022994803.1 (47562 bp) chr NW_022994804.1 (45312 bp) chr NW_022994805.1 (654836 bp) chr NW_022994806.1 (34204 bp) chr NW_022994807.1 (33063 bp) chr NW_022994808.1 (32339 bp) chr NW_022994809.1 (621026 bp) chr NW_022994810.1 (30983 bp) chr NW_022994811.1 (28060 bp) chr NW_022994812.1 (26205 bp) chr NW_022994813.1 (609159 bp) chr NW_022994814.1 (18830 bp) chr NW_022994815.1 (549086 bp) chr NW_022994816.1 (985078 bp) chr NW_022994817.1 (2254 bp) chr NW_022994818.1 (1361 bp) chr NW_022994819.1 (734241 bp) chr NW_022994820.1 (658371 bp) chr NW_022994821.1 (546250 bp) chr NW_022994822.1 (614137 bp) chr NW_022994823.1 (196267 bp) chr NW_022994824.1 (461872 bp) chr NW_022994825.1 (345626 bp) chr NW_022994826.1 (153136 bp) chr NW_022994827.1 (85676 bp) chr NW_022994828.1 (316174 bp) chr NW_022994829.1 (476514 bp) chr NW_022994830.1 (534456 bp) chr NW_022994831.1 (527944 bp) chr NW_022994832.1 (513312 bp) chr NW_022994833.1 (507370 bp) chr NW_022994834.1 (496827 bp) chr NW_022994835.1 (482992 bp) chr NW_022994836.1 (471557 bp) chr NW_022994837.1 (686402 bp) chr NW_022994838.1 (445523 bp) chr NW_022994839.1 (505355 bp) chr NW_022994840.1 (408464 bp) chr NW_022994841.1 (392916 bp) chr NW_022994842.1 (346530 bp) chr NW_022994843.1 (346498 bp) chr NW_022994844.1 (984115 bp) chr NW_022994845.1 (334217 bp) chr NW_022994846.1 (330898 bp) chr NW_022994847.1 (310459 bp) chr NW_022994848.1 (975996 bp) chr NW_022994849.1 (299473 bp) chr NW_022994850.1 (724080 bp) chr NW_022994851.1 (284019 bp) chr NW_022994852.1 (380988 bp) chr NW_022994853.1 (271986 bp) chr NW_022994854.1 (271335 bp) chr NW_022994855.1 (270660 bp) chr NW_022994856.1 (269814 bp) chr NW_022994857.1 (255287 bp) chr NW_022994858.1 (250265 bp) chr NW_022994859.1 (249553 bp) chr NW_022994860.1 (243901 bp) chr NW_022994861.1 (243737 bp) chr NW_022994862.1 (230837 bp) chr NW_022994863.1 (896916 bp) chr NW_022994864.1 (230075 bp) chr NW_022994865.1 (3851109 bp) chr NW_022994866.1 (222500 bp) chr NW_022994867.1 (221461 bp) chr NW_022994868.1 (214429 bp) chr NW_022994869.1 (208222 bp) chr NW_022994870.1 (984156 bp) chr NW_022994871.1 (303113 bp) chr NW_022994872.1 (195767 bp) chr NW_022994873.1 (192086 bp) chr NW_022994874.1 (189815 bp) chr NW_022994875.1 (180076 bp) chr NW_022994876.1 (178302 bp) chr NW_022994877.1 (371905 bp) chr NW_022994878.1 (173440 bp) chr NW_022994879.1 (171659 bp) chr NW_022994880.1 (169219 bp) chr NW_022994881.1 (520634 bp) chr NW_022994882.1 (167015 bp) chr NW_022994883.1 (166538 bp) chr NW_022994884.1 (165345 bp) chr NW_022994885.1 (161001 bp) chr NW_022994886.1 (803096 bp) chr NW_022994887.1 (153941 bp) chr NW_022994888.1 (153236 bp) chr NW_022994889.1 (151090 bp) chr NW_022994890.1 (226113 bp) chr NW_022994891.1 (142569 bp) chr NW_022994892.1 (139519 bp) chr NW_022994893.1 (137056 bp) chr NW_022994894.1 (135750 bp) chr NW_022994895.1 (800838 bp) chr NW_022994896.1 (123475 bp) chr NW_022994897.1 (543823 bp) chr NW_022994898.1 (63957 bp) chr NW_022994899.1 (135656 bp) chr NW_022994900.1 (158606 bp) chr NW_022994901.1 (138885 bp) chr NW_022994902.1 (213710 bp) chr NW_022994903.1 (31917 bp) chr NW_022994904.1 (192304 bp) chr NW_022994905.1 (122499 bp) chr NW_022994906.1 (24192 bp) chr NW_022994907.1 (80452 bp) chr NW_022994908.1 (34710 bp) chr NW_022994909.1 (80340 bp) chr NW_022994910.1 (59023 bp) chr NW_022994911.1 (90223 bp) chr NW_022994912.1 (80828 bp) chr NW_022994913.1 (18545 bp) chr NW_022994914.1 (79317 bp) chr NW_022994915.1 (76490 bp) chr NW_022994916.1 (77779 bp) chr NW_022994917.1 (39112 bp) chr NW_022994918.1 (404750 bp) chr NW_022994919.1 (196227 bp) chr NW_022994920.1 (39174 bp) chr NW_022994921.1 (323512 bp) chr NW_022994922.1 (83186 bp) chr NW_022994923.1 (61906 bp) chr NW_022994924.1 (127844 bp) chr NW_022994925.1 (61549 bp) chr NW_022994926.1 (81940 bp) chr NW_022994927.1 (162546 bp) chr NW_022994928.1 (69385 bp) chr NW_022994929.1 (46878 bp) chr NW_022994930.1 (145484 bp) chr NW_022994931.1 (118323 bp) chr NW_022994932.1 (123881 bp) chr NW_022994933.1 (29995 bp) chr NW_022994934.1 (161585 bp) chr NW_022994935.1 (43805 bp) chr NW_022994936.1 (297039 bp) chr NW_022994937.1 (490709 bp) chr NW_022994938.1 (203969 bp) chr NW_022994939.1 (324655 bp) chr NW_022994940.1 (218172 bp) chr NW_022994941.1 (19044 bp) chr NW_022994942.1 (61061 bp) chr NW_022994943.1 (289459 bp) chr NW_022994944.1 (261312 bp) chr NW_022994945.1 (625727 bp) chr NW_022994946.1 (333635 bp) chr NW_022994947.1 (135775 bp) chr NW_022994948.1 (858184 bp) chr NW_022994949.1 (121447 bp) chr NW_022994950.1 (33519 bp) chr NW_022994951.1 (187731 bp) chr NW_022994952.1 (219001 bp) chr NW_022994953.1 (45830 bp) chr NW_022994954.1 (129811 bp) chr NW_022994955.1 (365466 bp) chr NW_022994956.1 (433943 bp) chr NW_022994957.1 (201146 bp) chr NW_022994958.1 (172809 bp) chr NW_022994959.1 (64928 bp) chr NW_022994960.1 (137501 bp) chr NW_022994961.1 (155459 bp) chr NW_022994962.1 (175997 bp) chr NW_022994963.1 (286963 bp) chr NW_022994964.1 (245988 bp) chr NW_022994965.1 (30682 bp) chr NW_022994966.1 (514743 bp) chr NW_022994967.1 (56505 bp) chr NW_022994968.1 (91994 bp) chr NW_022994969.1 (256332 bp) chr NW_022994970.1 (36429 bp) chr NW_022994971.1 (30384 bp) chr NW_022994972.1 (189740 bp) chr NW_022994973.1 (66576 bp) chr NW_022994974.1 (36592 bp) chr NW_022994975.1 (74180 bp) chr NW_022994976.1 (30109 bp) chr NW_022994977.1 (141708 bp) chr NW_022994978.1 (113692 bp) chr NW_022994979.1 (83790 bp) chr NW_022994980.1 (6557 bp) chr NW_022994981.1 (62922 bp) chr NW_022994982.1 (153818 bp) chr NW_022994983.1 (79855 bp) chr NW_022994984.1 (42847 bp) chr NW_022994985.1 (190097 bp) chr NW_022994986.1 (135148 bp) chr NW_022994987.1 (316463 bp) chr NW_022994988.1 (28442 bp) chr NW_022994989.1 (147472 bp) chr NW_022994990.1 (30511 bp) chr NW_022994991.1 (237136 bp) chr NW_022994992.1 (107548 bp) chr NW_022994993.1 (225226 bp) chr NW_022994994.1 (24264 bp) chr NW_022994995.1 (63071 bp) chr NW_022994996.1 (98197 bp) chr NW_022994997.1 (297219 bp) chr NW_022994998.1 (55042 bp) chr NC_001276.1 (18224 bp) Single-core mode: setting pid to 1 Paired-end alignments will be performed ======================================= The provided filenames for paired-end alignments are /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R2.fq.gz Input files are in FastQ format Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R1.fq.gz Writing a C -> T converted version of the input file zrtg3644_9_R1.fq.gz to zrtg3644_9_R1.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_9_R1.fq.gz to zrtg3644_9_R1.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_9_R1.fq.gz (100001 sequences in total) Processing reads up to sequence no. 100000 from /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R2.fq.gz Writing a C -> T converted version of the input file zrtg3644_9_R2.fq.gz to zrtg3644_9_R2.fq.gz_C_to_T.fastq Writing a G -> A converted version of the input file zrtg3644_9_R2.fq.gz to zrtg3644_9_R2.fq.gz_G_to_A.fastq Created C -> T as well as G -> A converted versions of the FastQ file zrtg3644_9_R2.fq.gz (100001 sequences in total) Input files are zrtg3644_9_R1.fq.gz_C_to_T.fastq and zrtg3644_9_R1.fq.gz_G_to_A.fastq and zrtg3644_9_R2.fq.gz_C_to_T.fastq and zrtg3644_9_R2.fq.gz_G_to_A.fastq (FastQ) Now running 4 individual instances of Bowtie 2 against the bisulfite genome of /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ with the specified options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 Now starting a Bowtie 2 paired-end alignment for CTread1GAread2CTgenome (reading in sequences from zrtg3644_9_R1.fq.gz_C_to_T.fastq and zrtg3644_9_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:6008:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATTTTTATATTTTATATATTTATAAATTTAAATTAATTTTTTTTTAATTTTATATAATAAATAATTATAATTTTTATAATTTAAATAATAAAAAATATAAAATTAATTAATTAT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:6008:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TTTTTATAAATAAAAATATATTTTTTTTAATATATAATATAAATATTTTTAAAATAAATTTAAAAAATTTATAATTAATTAATTTTATATTTTTTATTATTTAAATTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2GAgenome (reading in sequences from zrtg3644_9_R1.fq.gz_G_to_A.fastq and zrtg3644_9_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --norc)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:6008:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATTTTTATATTCCACATACTTACAAATCTAAATCAACTCTTTTTTAATTTTACACAATAAATAACTATAATCTTTATAACTTAAATAATAAAAAACATAAAATTAATTAACCAC FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:6008:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TTTTTGTGAATAGAGATATGTTTTTTTTGATGTATGATGTAAATATTTTTGAAATGAATTTGAAAAGTTTGTGGTTAATTAATTTTATGTTTTTTATTATTTAAGTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for GAread1CTread2CTgenome (reading in sequences from zrtg3644_9_R1.fq.gz_G_to_A.fastq and zrtg3644_9_R2.fq.gz_C_to_T.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:6008:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATTTTTATATTCCACATACTTACAAATCTAAATCAACTCTTTTTTAATTTTACACAATAAATAACTATAATCTTTATAACTTAAATAATAAAAAACATAAAATTAATTAACCAC FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:6008:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TTTTTGTGAATAGAGATATGTTTTTTTTGATGTATGATGTAAATATTTTTGAAATGAATTTGAAAAGTTTGTGGTTAATTAATTTTATGTTTTTTATTATTTAAGTTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP Now starting a Bowtie 2 paired-end alignment for CTread1GAread2GAgenome (reading in sequences from zrtg3644_9_R1.fq.gz_C_to_T.fastq and zrtg3644_9_R2.fq.gz_G_to_A.fastq, with the options: -q --score-min L,0,-0.6 -p 4 --reorder --ignore-quals --no-mixed --no-discordant --dovetail --maxins 500 --nofw)) Found first alignment: A00742:173:HMGVGDSXY:2:1101:6008:1000_1:N:0:NGTCGCTG+AGTCAGAC/1 77 * 0 0 * * 0 0 ATTTTTATATTTTATATATTTATAAATTTAAATTAATTTTTTTTTAATTTTATATAATAAATAATTATAATTTTTATAATTTAAATAATAAAAAATATAAAATTAATTAATTAT FFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FF,FFFFF:FF:FF YT:Z:UP A00742:173:HMGVGDSXY:2:1101:6008:1000_2:N:0:NGTCGCTG+AGTCAGAC/2 141 * 0 0 * * 0 0 TTTTTATAAATAAAAATATATTTTTTTTAATATATAATATAAATATTTTTAAAATAAATTTAAAAAATTTATAATTAATTAATTTTATATTTTTTATTATTTAAATTATAA FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFF:FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF YT:Z:UP >>> Writing bisulfite mapping results to zrtg3644_9_R1_bismark_bt2_pe.bam <<< Reading in the sequence files /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R1.fq.gz and /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R2.fq.gz 100000 reads; of these: 100000 (100.00%) were paired; of these: 72580 (72.58%) aligned concordantly 0 times 11906 (11.91%) aligned concordantly exactly 1 time 15514 (15.51%) aligned concordantly >1 times 27.42% overall alignment rate 100000 reads; of these: 100000 (100.00%) were paired; of these: 72433 (72.43%) aligned concordantly 0 times 12034 (12.03%) aligned concordantly exactly 1 time 15533 (15.53%) aligned concordantly >1 times 27.57% overall alignment rate 100000 reads; of these: 100000 (100000100.00 reads; of these:% ) were paired; of these: 100000 (72738 (100.0072.74%%) were paired; of these:) aligned concordantly 0 times 7299111895 ( (72.9911.89%%) aligned concordantly 0 times) aligned concordantly exactly 1 time 1179515367 ( (11.7915.37%%) aligned concordantly exactly 1 time) aligned concordantly >1 times 27.2615214% ( overall alignment rate15.21 %) aligned concordantly >1 times 27.01% overall alignment rate Processed 100000 sequences in total Successfully deleted the temporary files zrtg3644_9_R1.fq.gz_C_to_T.fastq, zrtg3644_9_R1.fq.gz_G_to_A.fastq, zrtg3644_9_R2.fq.gz_C_to_T.fastq and zrtg3644_9_R2.fq.gz_G_to_A.fastq Final Alignment report ====================== Sequence pairs analysed in total: 100000 Number of paired-end alignments with a unique best hit: 60757 Mapping efficiency: 60.8% Sequence pairs with no alignments under any condition: 21589 Sequence pairs did not map uniquely: 17654 Sequence pairs which were discarded because genomic sequence could not be extracted: 0 Number of sequence pairs with unique best (first) alignment came from the bowtie output: CT/GA/CT: 15319 ((converted) top strand) GA/CT/CT: 14927 (complementary to (converted) top strand) GA/CT/GA: 15269 (complementary to (converted) bottom strand) CT/GA/GA: 15242 ((converted) bottom strand) Final Cytosine Methylation Report ================================= Total number of C's analysed: 2120011 Total methylated C's in CpG context: 30085 Total methylated C's in CHG context: 1759 Total methylated C's in CHH context: 7647 Total methylated C's in Unknown context: 80 Total unmethylated C's in CpG context: 246978 Total unmethylated C's in CHG context: 370481 Total unmethylated C's in CHH context: 1463061 Total unmethylated C's in Unknown context: 4956 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% C methylated in unknown context (CN or CHN): 1.6% Bismark completed in 0d 0h 0m 51s ==================== Bismark run complete ==================== Processing paired-end Bismark output file(s) (SAM format): 0501_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>0501_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 0501_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 0501_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 0501_R1_bismark_bt2_pe.bam: 59640 Total number duplicated alignments removed: 3083 (5.17%) Duplicated alignments were found at: 2972 different position(s) Total count of deduplicated leftover sequences: 56557 (94.83% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/0501_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0501_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 0502_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>0502_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 0502_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 0502_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 0502_R1_bismark_bt2_pe.bam: 59284 Total number duplicated alignments removed: 2824 (4.76%) Duplicated alignments were found at: 2747 different position(s) Total count of deduplicated leftover sequences: 56460 (95.24% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/0502_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0502_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 0503_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>0503_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 0503_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 0503_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 0503_R1_bismark_bt2_pe.bam: 59416 Total number duplicated alignments removed: 2994 (5.04%) Duplicated alignments were found at: 2901 different position(s) Total count of deduplicated leftover sequences: 56422 (94.96% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/0503_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0503_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 3501_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>3501_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 3501_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 3501_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 3501_R1_bismark_bt2_pe.bam: 60904 Total number duplicated alignments removed: 3124 (5.13%) Duplicated alignments were found at: 3038 different position(s) Total count of deduplicated leftover sequences: 57780 (94.87% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/3501_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3501_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 3502_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>3502_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 3502_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 3502_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 3502_R1_bismark_bt2_pe.bam: 61008 Total number duplicated alignments removed: 3289 (5.39%) Duplicated alignments were found at: 3173 different position(s) Total count of deduplicated leftover sequences: 57719 (94.61% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/3502_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3502_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 3503_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>3503_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 3503_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 3503_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 3503_R1_bismark_bt2_pe.bam: 57332 Total number duplicated alignments removed: 2434 (4.25%) Duplicated alignments were found at: 2364 different position(s) Total count of deduplicated leftover sequences: 54898 (95.75% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/3503_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3503_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5201_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>5201_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5201_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5201_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 5201_R1_bismark_bt2_pe.bam: 60895 Total number duplicated alignments removed: 3072 (5.04%) Duplicated alignments were found at: 2996 different position(s) Total count of deduplicated leftover sequences: 57823 (94.96% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5201_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5201_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5202_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>5202_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5202_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5202_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 5202_R1_bismark_bt2_pe.bam: 60899 Total number duplicated alignments removed: 2956 (4.85%) Duplicated alignments were found at: 2857 different position(s) Total count of deduplicated leftover sequences: 57943 (95.15% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5202_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5202_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5203_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>5203_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5203_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5203_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 5203_R1_bismark_bt2_pe.bam: 58371 Total number duplicated alignments removed: 2728 (4.67%) Duplicated alignments were found at: 2653 different position(s) Total count of deduplicated leftover sequences: 55643 (95.33% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5203_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5203_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5901_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>5901_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5901_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5901_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 5901_R1_bismark_bt2_pe.bam: 59788 Total number duplicated alignments removed: 3275 (5.48%) Duplicated alignments were found at: 3170 different position(s) Total count of deduplicated leftover sequences: 56513 (94.52% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5901_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5901_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5902_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>5902_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5902_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5902_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 5902_R1_bismark_bt2_pe.bam: 60658 Total number duplicated alignments removed: 3179 (5.24%) Duplicated alignments were found at: 3088 different position(s) Total count of deduplicated leftover sequences: 57479 (94.76% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5902_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5902_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): 5903_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>5903_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file 5903_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: 5903_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in 5903_R1_bismark_bt2_pe.bam: 59448 Total number duplicated alignments removed: 2372 (3.99%) Duplicated alignments were found at: 2305 different position(s) Total count of deduplicated leftover sequences: 57076 (96.01% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5903_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5903_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_10_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_10_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_10_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_10_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_10_R1_bismark_bt2_pe.bam: 61864 Total number duplicated alignments removed: 6408 (10.36%) Duplicated alignments were found at: 5806 different position(s) Total count of deduplicated leftover sequences: 55456 (89.64% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_10_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_1_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_1_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_1_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_1_R1_bismark_bt2_pe.bam: 61618 Total number duplicated alignments removed: 6726 (10.92%) Duplicated alignments were found at: 6009 different position(s) Total count of deduplicated leftover sequences: 54892 (89.08% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_2_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_2_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_2_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_2_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_2_R1_bismark_bt2_pe.bam: 61056 Total number duplicated alignments removed: 6107 (10.00%) Duplicated alignments were found at: 5542 different position(s) Total count of deduplicated leftover sequences: 54949 (90.00% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_3_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_3_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_3_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_3_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_3_R1_bismark_bt2_pe.bam: 60805 Total number duplicated alignments removed: 5850 (9.62%) Duplicated alignments were found at: 5361 different position(s) Total count of deduplicated leftover sequences: 54955 (90.38% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_3_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_4_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_4_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_4_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_4_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_4_R1_bismark_bt2_pe.bam: 61751 Total number duplicated alignments removed: 6492 (10.51%) Duplicated alignments were found at: 5909 different position(s) Total count of deduplicated leftover sequences: 55259 (89.49% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_4_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_5_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_5_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_5_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_5_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_5_R1_bismark_bt2_pe.bam: 61435 Total number duplicated alignments removed: 6349 (10.33%) Duplicated alignments were found at: 5759 different position(s) Total count of deduplicated leftover sequences: 55086 (89.67% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_6_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_6_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_6_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_6_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_6_R1_bismark_bt2_pe.bam: 60946 Total number duplicated alignments removed: 6386 (10.48%) Duplicated alignments were found at: 5727 different position(s) Total count of deduplicated leftover sequences: 54560 (89.52% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_6_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_7_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_7_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_7_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_7_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_7_R1_bismark_bt2_pe.bam: 61281 Total number duplicated alignments removed: 5803 (9.47%) Duplicated alignments were found at: 5250 different position(s) Total count of deduplicated leftover sequences: 55478 (90.53% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_7_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_8_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_8_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_8_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_8_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_8_R1_bismark_bt2_pe.bam: 61749 Total number duplicated alignments removed: 7118 (11.53%) Duplicated alignments were found at: 6389 different position(s) Total count of deduplicated leftover sequences: 54631 (88.47% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_8_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3534_9_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3534_9_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3534_9_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3534_9_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3534_9_R1_bismark_bt2_pe.bam: 61884 Total number duplicated alignments removed: 6157 (9.95%) Duplicated alignments were found at: 5596 different position(s) Total count of deduplicated leftover sequences: 55727 (90.05% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_9_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_10_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_10_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_10_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_10_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_10_R1_bismark_bt2_pe.bam: 61153 Total number duplicated alignments removed: 4006 (6.55%) Duplicated alignments were found at: 3715 different position(s) Total count of deduplicated leftover sequences: 57147 (93.45% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_10_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_11_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_11_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_11_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_11_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_11_R1_bismark_bt2_pe.bam: 60960 Total number duplicated alignments removed: 4074 (6.68%) Duplicated alignments were found at: 3795 different position(s) Total count of deduplicated leftover sequences: 56886 (93.32% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_11_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_12_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_12_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_12_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_12_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_12_R1_bismark_bt2_pe.bam: 61367 Total number duplicated alignments removed: 3889 (6.34%) Duplicated alignments were found at: 3658 different position(s) Total count of deduplicated leftover sequences: 57478 (93.66% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_12_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_13_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_13_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_13_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_13_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_13_R1_bismark_bt2_pe.bam: 61792 Total number duplicated alignments removed: 4450 (7.20%) Duplicated alignments were found at: 4165 different position(s) Total count of deduplicated leftover sequences: 57342 (92.80% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_13_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_14_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_14_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_14_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_14_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_14_R1_bismark_bt2_pe.bam: 62088 Total number duplicated alignments removed: 4054 (6.53%) Duplicated alignments were found at: 3786 different position(s) Total count of deduplicated leftover sequences: 58034 (93.47% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_15_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_15_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_15_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_15_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_15_R1_bismark_bt2_pe.bam: 61418 Total number duplicated alignments removed: 3982 (6.48%) Duplicated alignments were found at: 3767 different position(s) Total count of deduplicated leftover sequences: 57436 (93.52% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_15_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_16_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_16_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_16_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_16_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_16_R1_bismark_bt2_pe.bam: 61736 Total number duplicated alignments removed: 4307 (6.98%) Duplicated alignments were found at: 4033 different position(s) Total count of deduplicated leftover sequences: 57429 (93.02% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_16_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_17_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_17_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_17_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_17_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_17_R1_bismark_bt2_pe.bam: 61805 Total number duplicated alignments removed: 4403 (7.12%) Duplicated alignments were found at: 4086 different position(s) Total count of deduplicated leftover sequences: 57402 (92.88% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_17_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_18_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_18_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_18_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_18_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_18_R1_bismark_bt2_pe.bam: 62397 Total number duplicated alignments removed: 3891 (6.24%) Duplicated alignments were found at: 3610 different position(s) Total count of deduplicated leftover sequences: 58506 (93.76% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_18_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_19_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_19_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_19_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_19_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_19_R1_bismark_bt2_pe.bam: 61402 Total number duplicated alignments removed: 3620 (5.90%) Duplicated alignments were found at: 3430 different position(s) Total count of deduplicated leftover sequences: 57782 (94.10% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_19_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_1_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_1_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_1_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_1_R1_bismark_bt2_pe.bam: 62534 Total number duplicated alignments removed: 4122 (6.59%) Duplicated alignments were found at: 3862 different position(s) Total count of deduplicated leftover sequences: 58412 (93.41% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_1_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_20_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_20_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_20_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_20_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_20_R1_bismark_bt2_pe.bam: 61592 Total number duplicated alignments removed: 4189 (6.80%) Duplicated alignments were found at: 3896 different position(s) Total count of deduplicated leftover sequences: 57403 (93.20% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_20_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_21_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_21_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_21_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_21_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_21_R1_bismark_bt2_pe.bam: 61354 Total number duplicated alignments removed: 4196 (6.84%) Duplicated alignments were found at: 3916 different position(s) Total count of deduplicated leftover sequences: 57158 (93.16% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_21_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_22_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_22_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_22_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_22_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_22_R1_bismark_bt2_pe.bam: 61838 Total number duplicated alignments removed: 4048 (6.55%) Duplicated alignments were found at: 3784 different position(s) Total count of deduplicated leftover sequences: 57790 (93.45% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_22_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_23_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_23_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_23_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_23_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_23_R1_bismark_bt2_pe.bam: 61316 Total number duplicated alignments removed: 4107 (6.70%) Duplicated alignments were found at: 3847 different position(s) Total count of deduplicated leftover sequences: 57209 (93.30% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_23_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_24_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_24_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_24_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_24_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_24_R1_bismark_bt2_pe.bam: 62315 Total number duplicated alignments removed: 4182 (6.71%) Duplicated alignments were found at: 3943 different position(s) Total count of deduplicated leftover sequences: 58133 (93.29% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_24_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_2_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_2_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_2_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_2_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_2_R1_bismark_bt2_pe.bam: 61033 Total number duplicated alignments removed: 4139 (6.78%) Duplicated alignments were found at: 3852 different position(s) Total count of deduplicated leftover sequences: 56894 (93.22% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_3_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_3_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_3_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_3_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_3_R1_bismark_bt2_pe.bam: 61161 Total number duplicated alignments removed: 3670 (6.00%) Duplicated alignments were found at: 3431 different position(s) Total count of deduplicated leftover sequences: 57491 (94.00% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_3_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_4_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_4_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_4_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_4_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_4_R1_bismark_bt2_pe.bam: 61250 Total number duplicated alignments removed: 4161 (6.79%) Duplicated alignments were found at: 3910 different position(s) Total count of deduplicated leftover sequences: 57089 (93.21% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_4_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_5_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_5_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_5_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_5_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_5_R1_bismark_bt2_pe.bam: 61442 Total number duplicated alignments removed: 3845 (6.26%) Duplicated alignments were found at: 3605 different position(s) Total count of deduplicated leftover sequences: 57597 (93.74% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_5_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_6_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_6_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_6_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_6_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_6_R1_bismark_bt2_pe.bam: 61890 Total number duplicated alignments removed: 3916 (6.33%) Duplicated alignments were found at: 3647 different position(s) Total count of deduplicated leftover sequences: 57974 (93.67% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_6_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_7_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_7_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_7_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_7_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_7_R1_bismark_bt2_pe.bam: 60610 Total number duplicated alignments removed: 3499 (5.77%) Duplicated alignments were found at: 3310 different position(s) Total count of deduplicated leftover sequences: 57111 (94.23% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_7_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_8_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_8_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_8_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_8_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_8_R1_bismark_bt2_pe.bam: 61057 Total number duplicated alignments removed: 3698 (6.06%) Duplicated alignments were found at: 3477 different position(s) Total count of deduplicated leftover sequences: 57359 (93.94% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_8_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zr3644_9_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zr3644_9_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zr3644_9_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zr3644_9_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zr3644_9_R1_bismark_bt2_pe.bam: 61092 Total number duplicated alignments removed: 4373 (7.16%) Duplicated alignments were found at: 4076 different position(s) Total count of deduplicated leftover sequences: 56719 (92.84% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3616_1_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3616_1_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3616_1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3616_1_R1_bismark_bt2_pe.bam: 62078 Total number duplicated alignments removed: 7811 (12.58%) Duplicated alignments were found at: 6700 different position(s) Total count of deduplicated leftover sequences: 54267 (87.42% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3616_2_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3616_2_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3616_2_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3616_2_R1_bismark_bt2_pe.bam: 61847 Total number duplicated alignments removed: 7757 (12.54%) Duplicated alignments were found at: 6637 different position(s) Total count of deduplicated leftover sequences: 54090 (87.46% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3616_3_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3616_3_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3616_3_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3616_3_R1_bismark_bt2_pe.bam: 61506 Total number duplicated alignments removed: 7768 (12.63%) Duplicated alignments were found at: 6710 different position(s) Total count of deduplicated leftover sequences: 53738 (87.37% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3616_4_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3616_4_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3616_4_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3616_4_R1_bismark_bt2_pe.bam: 61653 Total number duplicated alignments removed: 7721 (12.52%) Duplicated alignments were found at: 6649 different position(s) Total count of deduplicated leftover sequences: 53932 (87.48% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3616_5_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3616_5_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3616_5_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3616_5_R1_bismark_bt2_pe.bam: 61681 Total number duplicated alignments removed: 7372 (11.95%) Duplicated alignments were found at: 6394 different position(s) Total count of deduplicated leftover sequences: 54309 (88.05% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3616_6_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3616_6_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3616_6_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3616_6_R1_bismark_bt2_pe.bam: 61511 Total number duplicated alignments removed: 8623 (14.02%) Duplicated alignments were found at: 7254 different position(s) Total count of deduplicated leftover sequences: 52888 (85.98% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3616_7_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3616_7_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3616_7_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3616_7_R1_bismark_bt2_pe.bam: 61554 Total number duplicated alignments removed: 7609 (12.36%) Duplicated alignments were found at: 6539 different position(s) Total count of deduplicated leftover sequences: 53945 (87.64% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3616_8_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3616_8_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3616_8_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3616_8_R1_bismark_bt2_pe.bam: 61458 Total number duplicated alignments removed: 7466 (12.15%) Duplicated alignments were found at: 6463 different position(s) Total count of deduplicated leftover sequences: 53992 (87.85% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_10_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_10_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_10_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_10_R1_bismark_bt2_pe.bam: 60926 Total number duplicated alignments removed: 3980 (6.53%) Duplicated alignments were found at: 3685 different position(s) Total count of deduplicated leftover sequences: 56946 (93.47% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_11_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_11_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_11_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_11_R1_bismark_bt2_pe.bam: 60730 Total number duplicated alignments removed: 4045 (6.66%) Duplicated alignments were found at: 3763 different position(s) Total count of deduplicated leftover sequences: 56685 (93.34% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_12_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_12_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_12_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_12_R1_bismark_bt2_pe.bam: 61267 Total number duplicated alignments removed: 3910 (6.38%) Duplicated alignments were found at: 3678 different position(s) Total count of deduplicated leftover sequences: 57357 (93.62% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_13_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_13_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_13_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_13_R1_bismark_bt2_pe.bam: 61532 Total number duplicated alignments removed: 4439 (7.21%) Duplicated alignments were found at: 4149 different position(s) Total count of deduplicated leftover sequences: 57093 (92.79% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_14_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_14_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_14_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_14_R1_bismark_bt2_pe.bam: 61818 Total number duplicated alignments removed: 4026 (6.51%) Duplicated alignments were found at: 3759 different position(s) Total count of deduplicated leftover sequences: 57792 (93.49% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_15_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_15_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_15_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_15_R1_bismark_bt2_pe.bam: 61239 Total number duplicated alignments removed: 3951 (6.45%) Duplicated alignments were found at: 3740 different position(s) Total count of deduplicated leftover sequences: 57288 (93.55% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_16_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_16_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_16_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_16_R1_bismark_bt2_pe.bam: 61417 Total number duplicated alignments removed: 4318 (7.03%) Duplicated alignments were found at: 4050 different position(s) Total count of deduplicated leftover sequences: 57099 (92.97% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_17_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_17_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_17_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_17_R1_bismark_bt2_pe.bam: 61619 Total number duplicated alignments removed: 4366 (7.09%) Duplicated alignments were found at: 4052 different position(s) Total count of deduplicated leftover sequences: 57253 (92.91% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_18_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_18_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_18_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_18_R1_bismark_bt2_pe.bam: 62205 Total number duplicated alignments removed: 3895 (6.26%) Duplicated alignments were found at: 3609 different position(s) Total count of deduplicated leftover sequences: 58310 (93.74% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_19_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_19_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_19_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_19_R1_bismark_bt2_pe.bam: 61076 Total number duplicated alignments removed: 3602 (5.90%) Duplicated alignments were found at: 3417 different position(s) Total count of deduplicated leftover sequences: 57474 (94.10% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_1_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_1_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_1_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_1_R1_bismark_bt2_pe.bam: 62198 Total number duplicated alignments removed: 4095 (6.58%) Duplicated alignments were found at: 3834 different position(s) Total count of deduplicated leftover sequences: 58103 (93.42% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_20_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_20_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_20_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_20_R1_bismark_bt2_pe.bam: 61432 Total number duplicated alignments removed: 4164 (6.78%) Duplicated alignments were found at: 3878 different position(s) Total count of deduplicated leftover sequences: 57268 (93.22% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_21_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_21_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_21_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_21_R1_bismark_bt2_pe.bam: 61032 Total number duplicated alignments removed: 4142 (6.79%) Duplicated alignments were found at: 3865 different position(s) Total count of deduplicated leftover sequences: 56890 (93.21% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_22_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_22_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_22_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_22_R1_bismark_bt2_pe.bam: 61648 Total number duplicated alignments removed: 4027 (6.53%) Duplicated alignments were found at: 3762 different position(s) Total count of deduplicated leftover sequences: 57621 (93.47% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_23_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_23_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_23_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_23_R1_bismark_bt2_pe.bam: 61099 Total number duplicated alignments removed: 4081 (6.68%) Duplicated alignments were found at: 3824 different position(s) Total count of deduplicated leftover sequences: 57018 (93.32% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_24_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_24_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_24_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_24_R1_bismark_bt2_pe.bam: 62084 Total number duplicated alignments removed: 4188 (6.75%) Duplicated alignments were found at: 3945 different position(s) Total count of deduplicated leftover sequences: 57896 (93.25% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_2_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_2_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_2_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_2_R1_bismark_bt2_pe.bam: 60791 Total number duplicated alignments removed: 4125 (6.79%) Duplicated alignments were found at: 3834 different position(s) Total count of deduplicated leftover sequences: 56666 (93.21% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_3_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_3_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_3_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_3_R1_bismark_bt2_pe.bam: 60870 Total number duplicated alignments removed: 3648 (5.99%) Duplicated alignments were found at: 3414 different position(s) Total count of deduplicated leftover sequences: 57222 (94.01% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_4_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_4_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_4_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_4_R1_bismark_bt2_pe.bam: 61001 Total number duplicated alignments removed: 4118 (6.75%) Duplicated alignments were found at: 3871 different position(s) Total count of deduplicated leftover sequences: 56883 (93.25% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_5_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_5_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_5_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_5_R1_bismark_bt2_pe.bam: 61139 Total number duplicated alignments removed: 3819 (6.25%) Duplicated alignments were found at: 3578 different position(s) Total count of deduplicated leftover sequences: 57320 (93.75% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_6_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_6_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_6_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_6_R1_bismark_bt2_pe.bam: 61547 Total number duplicated alignments removed: 3885 (6.31%) Duplicated alignments were found at: 3613 different position(s) Total count of deduplicated leftover sequences: 57662 (93.69% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_7_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_7_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_7_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_7_R1_bismark_bt2_pe.bam: 60320 Total number duplicated alignments removed: 3475 (5.76%) Duplicated alignments were found at: 3290 different position(s) Total count of deduplicated leftover sequences: 56845 (94.24% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ SN:NW_022994941.1 LN:19044 skipping header line: @SQ SN:NW_022994942.1 LN:61061 skipping header line: @SQ SN:NW_022994943.1 LN:289459 skipping header line: @SQ SN:NW_022994944.1 LN:261312 skipping header line: @SQ SN:NW_022994945.1 LN:625727 skipping header line: @SQ SN:NW_022994946.1 LN:333635 skipping header line: @SQ SN:NW_022994947.1 LN:135775 skipping header line: @SQ SN:NW_022994948.1 LN:858184 skipping header line: @SQ SN:NW_022994949.1 LN:121447 skipping header line: @SQ SN:NW_022994950.1 LN:33519 skipping header line: @SQ SN:NW_022994951.1 LN:187731 skipping header line: @SQ SN:NW_022994952.1 LN:219001 skipping header line: @SQ SN:NW_022994953.1 LN:45830 skipping header line: @SQ SN:NW_022994954.1 LN:129811 skipping header line: @SQ SN:NW_022994955.1 LN:365466 skipping header line: @SQ SN:NW_022994956.1 LN:433943 skipping header line: @SQ SN:NW_022994957.1 LN:201146 skipping header line: @SQ SN:NW_022994958.1 LN:172809 skipping header line: @SQ SN:NW_022994959.1 LN:64928 skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_8_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_8_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_8_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ SN:NW_022994779.1 LN:111600 skipping header line: @SQ SN:NW_022994780.1 LN:109880 skipping header line: @SQ SN:NW_022994781.1 LN:109004 skipping header line: @SQ SN:NW_022994782.1 LN:105193 skipping header line: @SQ SN:NW_022994783.1 LN:103107 skipping header line: @SQ SN:NW_022994784.1 LN:1334230 skipping header line: @SQ SN:NW_022994785.1 LN:99559 skipping header line: @SQ SN:NW_022994786.1 LN:93417 skipping header line: @SQ SN:NW_022994787.1 LN:85616 skipping header line: @SQ SN:NW_022994788.1 LN:84435 skipping header line: @SQ SN:NW_022994789.1 LN:725421 skipping header line: @SQ SN:NW_022994790.1 LN:78344 skipping header line: @SQ SN:NW_022994791.1 LN:77172 skipping header line: @SQ SN:NW_022994792.1 LN:66789 skipping header line: @SQ SN:NW_022994793.1 LN:66084 skipping header line: @SQ SN:NW_022994794.1 LN:699037 skipping header line: @SQ SN:NW_022994795.1 LN:63125 skipping header line: @SQ SN:NW_022994796.1 LN:62774 skipping header line: @SQ SN:NW_022994797.1 LN:60186 skipping header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: @SQ SN:NW_022994835.1 LN:482992 skipping header line: @SQ SN:NW_022994836.1 LN:471557 skipping header line: @SQ SN:NW_022994837.1 LN:686402 skipping header line: @SQ SN:NW_022994838.1 LN:445523 skipping header line: @SQ SN:NW_022994839.1 LN:505355 skipping header line: @SQ SN:NW_022994840.1 LN:408464 skipping header line: @SQ SN:NW_022994841.1 LN:392916 skipping header line: @SQ SN:NW_022994842.1 LN:346530 skipping header line: @SQ SN:NW_022994843.1 LN:346498 skipping header line: @SQ SN:NW_022994844.1 LN:984115 skipping header line: @SQ SN:NW_022994845.1 LN:334217 skipping header line: @SQ SN:NW_022994846.1 LN:330898 skipping header line: @SQ SN:NW_022994847.1 LN:310459 skipping header line: @SQ SN:NW_022994848.1 LN:975996 skipping header line: @SQ SN:NW_022994849.1 LN:299473 skipping header line: @SQ SN:NW_022994850.1 LN:724080 skipping header line: @SQ SN:NW_022994851.1 LN:284019 skipping header line: @SQ SN:NW_022994852.1 LN:380988 skipping header line: @SQ SN:NW_022994853.1 LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_8_R1_bismark_bt2_pe.bam: 60857 Total number duplicated alignments removed: 3692 (6.07%) Duplicated alignments were found at: 3470 different position(s) Total count of deduplicated leftover sequences: 57165 (93.93% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R2.fq.gz" Processing paired-end Bismark output file(s) (SAM format): zrtg3644_9_R1_bismark_bt2_pe.bam If there are several alignments to a single position in the genome the first alignment will be chosen. Since the input files are not in any way sorted this is a near-enough random selection of reads. Checking file >>zrtg3644_9_R1_bismark_bt2_pe.bam<< for signs of file truncation... Now testing Bismark result file zrtg3644_9_R1_bismark_bt2_pe.bam for positional sorting (which would be bad...) ...passed! Output file is: zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam skipping header line: @HD VN:1.0 SO:unsorted skipping header line: @SQ SN:NC_047559.1 LN:55785328 skipping header line: @SQ SN:NC_047560.1 LN:73222313 skipping header line: @SQ SN:NC_047561.1 LN:58319100 skipping header line: @SQ SN:NC_047562.1 LN:53127865 skipping header line: @SQ SN:NC_047563.1 LN:73550375 skipping header line: @SQ SN:NC_047564.1 LN:60151564 skipping header line: @SQ SN:NC_047565.1 LN:62107823 skipping header line: @SQ SN:NC_047566.1 LN:58462999 skipping header line: @SQ SN:NC_047567.1 LN:37089910 skipping header line: @SQ SN:NC_047568.1 LN:57541580 skipping header line: @SQ SN:NW_022994773.1 LN:129571 skipping header line: @SQ SN:NW_022994774.1 LN:1185781 skipping header line: @SQ SN:NW_022994775.1 LN:128451 skipping header line: @SQ SN:NW_022994776.1 LN:124569 skipping header line: @SQ SN:NW_022994777.1 LN:123505 skipping header line: @SQ SN:NW_022994778.1 LN:761972 skipping header line: @SQ 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header line: @SQ SN:NW_022994798.1 LN:59881 skipping header line: @SQ SN:NW_022994799.1 LN:680695 skipping header line: @SQ SN:NW_022994800.1 LN:57426 skipping header line: @SQ SN:NW_022994801.1 LN:56398 skipping header line: @SQ SN:NW_022994802.1 LN:52255 skipping header line: @SQ SN:NW_022994803.1 LN:47562 skipping header line: @SQ SN:NW_022994804.1 LN:45312 skipping header line: @SQ SN:NW_022994805.1 LN:654836 skipping header line: @SQ SN:NW_022994806.1 LN:34204 skipping header line: @SQ SN:NW_022994807.1 LN:33063 skipping header line: @SQ SN:NW_022994808.1 LN:32339 skipping header line: @SQ SN:NW_022994809.1 LN:621026 skipping header line: @SQ SN:NW_022994810.1 LN:30983 skipping header line: @SQ SN:NW_022994811.1 LN:28060 skipping header line: @SQ SN:NW_022994812.1 LN:26205 skipping header line: @SQ SN:NW_022994813.1 LN:609159 skipping header line: @SQ SN:NW_022994814.1 LN:18830 skipping header line: @SQ SN:NW_022994815.1 LN:549086 skipping header line: @SQ SN:NW_022994816.1 LN:985078 skipping header line: @SQ SN:NW_022994817.1 LN:2254 skipping header line: @SQ SN:NW_022994818.1 LN:1361 skipping header line: @SQ SN:NW_022994819.1 LN:734241 skipping header line: @SQ SN:NW_022994820.1 LN:658371 skipping header line: @SQ SN:NW_022994821.1 LN:546250 skipping header line: @SQ SN:NW_022994822.1 LN:614137 skipping header line: @SQ SN:NW_022994823.1 LN:196267 skipping header line: @SQ SN:NW_022994824.1 LN:461872 skipping header line: @SQ SN:NW_022994825.1 LN:345626 skipping header line: @SQ SN:NW_022994826.1 LN:153136 skipping header line: @SQ SN:NW_022994827.1 LN:85676 skipping header line: @SQ SN:NW_022994828.1 LN:316174 skipping header line: @SQ SN:NW_022994829.1 LN:476514 skipping header line: @SQ SN:NW_022994830.1 LN:534456 skipping header line: @SQ SN:NW_022994831.1 LN:527944 skipping header line: @SQ SN:NW_022994832.1 LN:513312 skipping header line: @SQ SN:NW_022994833.1 LN:507370 skipping header line: @SQ SN:NW_022994834.1 LN:496827 skipping header line: 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LN:271986 skipping header line: @SQ SN:NW_022994854.1 LN:271335 skipping header line: @SQ SN:NW_022994855.1 LN:270660 skipping header line: @SQ SN:NW_022994856.1 LN:269814 skipping header line: @SQ SN:NW_022994857.1 LN:255287 skipping header line: @SQ SN:NW_022994858.1 LN:250265 skipping header line: @SQ SN:NW_022994859.1 LN:249553 skipping header line: @SQ SN:NW_022994860.1 LN:243901 skipping header line: @SQ SN:NW_022994861.1 LN:243737 skipping header line: @SQ SN:NW_022994862.1 LN:230837 skipping header line: @SQ SN:NW_022994863.1 LN:896916 skipping header line: @SQ SN:NW_022994864.1 LN:230075 skipping header line: @SQ SN:NW_022994865.1 LN:3851109 skipping header line: @SQ SN:NW_022994866.1 LN:222500 skipping header line: @SQ SN:NW_022994867.1 LN:221461 skipping header line: @SQ SN:NW_022994868.1 LN:214429 skipping header line: @SQ SN:NW_022994869.1 LN:208222 skipping header line: @SQ SN:NW_022994870.1 LN:984156 skipping header line: @SQ SN:NW_022994871.1 LN:303113 skipping header line: @SQ SN:NW_022994872.1 LN:195767 skipping header line: @SQ SN:NW_022994873.1 LN:192086 skipping header line: @SQ SN:NW_022994874.1 LN:189815 skipping header line: @SQ SN:NW_022994875.1 LN:180076 skipping header line: @SQ SN:NW_022994876.1 LN:178302 skipping header line: @SQ SN:NW_022994877.1 LN:371905 skipping header line: @SQ SN:NW_022994878.1 LN:173440 skipping header line: @SQ SN:NW_022994879.1 LN:171659 skipping header line: @SQ SN:NW_022994880.1 LN:169219 skipping header line: @SQ SN:NW_022994881.1 LN:520634 skipping header line: @SQ SN:NW_022994882.1 LN:167015 skipping header line: @SQ SN:NW_022994883.1 LN:166538 skipping header line: @SQ SN:NW_022994884.1 LN:165345 skipping header line: @SQ SN:NW_022994885.1 LN:161001 skipping header line: @SQ SN:NW_022994886.1 LN:803096 skipping header line: @SQ SN:NW_022994887.1 LN:153941 skipping header line: @SQ SN:NW_022994888.1 LN:153236 skipping header line: @SQ SN:NW_022994889.1 LN:151090 skipping header line: @SQ SN:NW_022994890.1 LN:226113 skipping header line: @SQ SN:NW_022994891.1 LN:142569 skipping header line: @SQ SN:NW_022994892.1 LN:139519 skipping header line: @SQ SN:NW_022994893.1 LN:137056 skipping header line: @SQ SN:NW_022994894.1 LN:135750 skipping header line: @SQ SN:NW_022994895.1 LN:800838 skipping header line: @SQ SN:NW_022994896.1 LN:123475 skipping header line: @SQ SN:NW_022994897.1 LN:543823 skipping header line: @SQ SN:NW_022994898.1 LN:63957 skipping header line: @SQ SN:NW_022994899.1 LN:135656 skipping header line: @SQ SN:NW_022994900.1 LN:158606 skipping header line: @SQ SN:NW_022994901.1 LN:138885 skipping header line: @SQ SN:NW_022994902.1 LN:213710 skipping header line: @SQ SN:NW_022994903.1 LN:31917 skipping header line: @SQ SN:NW_022994904.1 LN:192304 skipping header line: @SQ SN:NW_022994905.1 LN:122499 skipping header line: @SQ SN:NW_022994906.1 LN:24192 skipping header line: @SQ SN:NW_022994907.1 LN:80452 skipping header line: @SQ SN:NW_022994908.1 LN:34710 skipping header line: @SQ SN:NW_022994909.1 LN:80340 skipping header line: @SQ SN:NW_022994910.1 LN:59023 skipping header line: @SQ SN:NW_022994911.1 LN:90223 skipping header line: @SQ SN:NW_022994912.1 LN:80828 skipping header line: @SQ SN:NW_022994913.1 LN:18545 skipping header line: @SQ SN:NW_0229949 Total number of alignments analysed in zrtg3644_9_R1_bismark_bt2_pe.bam: 60757 Total number duplicated alignments removed: 4364 (7.18%) Duplicated alignments were found at: 4061 different position(s) Total count of deduplicated leftover sequences: 56393 (92.82% of total) 14.1 LN:79317 skipping header line: @SQ SN:NW_022994915.1 LN:76490 skipping header line: @SQ SN:NW_022994916.1 LN:77779 skipping header line: @SQ SN:NW_022994917.1 LN:39112 skipping header line: @SQ SN:NW_022994918.1 LN:404750 skipping header line: @SQ SN:NW_022994919.1 LN:196227 skipping header line: @SQ SN:NW_022994920.1 LN:39174 skipping header line: @SQ SN:NW_022994921.1 LN:323512 skipping header line: @SQ SN:NW_022994922.1 LN:83186 skipping header line: @SQ SN:NW_022994923.1 LN:61906 skipping header line: @SQ SN:NW_022994924.1 LN:127844 skipping header line: @SQ SN:NW_022994925.1 LN:61549 skipping header line: @SQ SN:NW_022994926.1 LN:81940 skipping header line: @SQ SN:NW_022994927.1 LN:162546 skipping header line: @SQ SN:NW_022994928.1 LN:69385 skipping header line: @SQ SN:NW_022994929.1 LN:46878 skipping header line: @SQ SN:NW_022994930.1 LN:145484 skipping header line: @SQ SN:NW_022994931.1 LN:118323 skipping header line: @SQ SN:NW_022994932.1 LN:123881 skipping header line: @SQ SN:NW_022994933.1 LN:29995 skipping header line: @SQ SN:NW_022994934.1 LN:161585 skipping header line: @SQ SN:NW_022994935.1 LN:43805 skipping header line: @SQ SN:NW_022994936.1 LN:297039 skipping header line: @SQ SN:NW_022994937.1 LN:490709 skipping header line: @SQ SN:NW_022994938.1 LN:203969 skipping header line: @SQ SN:NW_022994939.1 LN:324655 skipping header line: @SQ SN:NW_022994940.1 LN:218172 skipping header line: @SQ 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skipping header line: @SQ SN:NW_022994960.1 LN:137501 skipping header line: @SQ SN:NW_022994961.1 LN:155459 skipping header line: @SQ SN:NW_022994962.1 LN:175997 skipping header line: @SQ SN:NW_022994963.1 LN:286963 skipping header line: @SQ SN:NW_022994964.1 LN:245988 skipping header line: @SQ SN:NW_022994965.1 LN:30682 skipping header line: @SQ SN:NW_022994966.1 LN:514743 skipping header line: @SQ SN:NW_022994967.1 LN:56505 skipping header line: @SQ SN:NW_022994968.1 LN:91994 skipping header line: @SQ SN:NW_022994969.1 LN:256332 skipping header line: @SQ SN:NW_022994970.1 LN:36429 skipping header line: @SQ SN:NW_022994971.1 LN:30384 skipping header line: @SQ SN:NW_022994972.1 LN:189740 skipping header line: @SQ SN:NW_022994973.1 LN:66576 skipping header line: @SQ SN:NW_022994974.1 LN:36592 skipping header line: @SQ SN:NW_022994975.1 LN:74180 skipping header line: @SQ SN:NW_022994976.1 LN:30109 skipping header line: @SQ SN:NW_022994977.1 LN:141708 skipping header line: @SQ SN:NW_022994978.1 LN:113692 skipping header line: @SQ SN:NW_022994979.1 LN:83790 skipping header line: @SQ SN:NW_022994980.1 LN:6557 skipping header line: @SQ SN:NW_022994981.1 LN:62922 skipping header line: @SQ SN:NW_022994982.1 LN:153818 skipping header line: @SQ SN:NW_022994983.1 LN:79855 skipping header line: @SQ SN:NW_022994984.1 LN:42847 skipping header line: @SQ SN:NW_022994985.1 LN:190097 skipping header line: @SQ SN:NW_022994986.1 LN:135148 skipping header line: @SQ SN:NW_022994987.1 LN:316463 skipping header line: @SQ SN:NW_022994988.1 LN:28442 skipping header line: @SQ SN:NW_022994989.1 LN:147472 skipping header line: @SQ SN:NW_022994990.1 LN:30511 skipping header line: @SQ SN:NW_022994991.1 LN:237136 skipping header line: @SQ SN:NW_022994992.1 LN:107548 skipping header line: @SQ SN:NW_022994993.1 LN:225226 skipping header line: @SQ SN:NW_022994994.1 LN:24264 skipping header line: @SQ SN:NW_022994995.1 LN:63071 skipping header line: @SQ SN:NW_022994996.1 LN:98197 skipping header line: @SQ SN:NW_022994997.1 LN:297219 skipping header line: @SQ SN:NW_022994998.1 LN:55042 skipping header line: @SQ SN:NC_001276.1 LN:18224 skipping header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R2.fq.gz" *** Bismark methylation extractor version v0.22.3 *** Trying to determine the type of mapping from the SAM header line of file 0501_R1_bismark_bt2_pe.deduplicated.bam Treating file(s) as paired-end data (as extracted from @PG line) Setting option '--no_overlap' since this is (normally) the right thing to do for paired-end data Core usage currently set to more than 20 threads. Let's see how this goes... (set value: 28) Summarising Bismark methylation extractor parameters: =============================================================== Bismark paired-end SAM format specified (default) Number of cores to be used: 28 Output will be written to the current directory ('/gscratch/scrubbed/sr320/060921-bigC') Summarising bedGraph parameters: =============================================================== Generating additional output in bedGraph and coverage format bedGraph format: coverage format: Using a cutoff of 1 read(s) to report cytosine positions Reporting and sorting cytosine methylation information in CpG context only (default) The bedGraph UNIX sort command will use the following memory setting: '75%'. Temporary directory used for sorting is the output directory Checking file >>0501_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >0501_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_0501_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 Now reading in Bismark result file 0501_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/0501_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0501_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56557 lines in total Total number of methylation call strings processed: 113114 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1859705 Total methylated C's in CpG context: 29965 Total methylated C's in CHG context: 2901 Total methylated C's in CHH context: 13262 Total C to T conversions in CpG context: 193629 Total C to T conversions in CHG context: 301308 Total C to T conversions in CHH context: 1318640 C methylated in CpG context: 13.4% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_0501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_0501_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_0501_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_0501_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_0501_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_0501_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_0501_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 0501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_0501_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_0501_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 0501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 0501_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 0501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_0501_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_0501_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_0501_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_0501_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 0501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 0501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>0502_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >0502_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_0502_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/0502_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0502_R2.fq.gz" Now reading in Bismark result file 0502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56460 lines in total Total number of methylation call strings processed: 112920 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1880911 Total methylated C's in CpG context: 29142 Total methylated C's in CHG context: 3310 Total methylated C's in CHH context: 13974 Total C to T conversions in CpG context: 193905 Total C to T conversions in CHG context: 305640 Total C to T conversions in CHH context: 1334940 C methylated in CpG context: 13.1% C methylated in CHG context: 1.1% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_0502_R1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_0502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_0502_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_0502_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_0502_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_0502_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_0502_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_0502_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_0502_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_0502_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 0502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_0502_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_0502_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 0502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 0502_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 0502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_0502_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_0502_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_0502_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 0502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 0502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>0503_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >0503_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_0503_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 0503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/0503_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/0503_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56422 lines in total Total number of methylation call strings processed: 112844 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1849861 Total methylated C's in CpG context: 31012 Total methylated C's in CHG context: 3012 Total methylated C's in CHH context: 14206 Total C to T conversions in CpG context: 187357 Total C to T conversions in CHG context: 296163 Total C to T conversions in CHH context: 1318111 C methylated in CpG context: 14.2% C methylated in CHG context: 1.0% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_0503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_0503_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_0503_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_0503_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_0503_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_0503_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_0503_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 0503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_0503_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_0503_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 0503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 0503_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 0503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_0503_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_0503_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_0503_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_0503_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 0503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 0503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>3501_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >3501_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_3501_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_3501_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3501_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/3501_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3501_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57780 lines in total Total number of methylation call strings processed: 115560 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1860250 Total methylated C's in CpG context: 27690 Total methylated C's in CHG context: 3151 Total methylated C's in CHH context: 13309 Total C to T conversions in CpG context: 194133 Total C to T conversions in CHG context: 298113 Total C to T conversions in CHH context: 1323854 C methylated in CpG context: 12.5% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_3501_R1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_OB_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_3501_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_3501_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_3501_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_3501_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_3501_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_3501_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_3501_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_3501_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_3501_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 3501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_3501_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_3501_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 3501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 3501_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 3501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_3501_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_3501_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_3501_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 3501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 3501_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>3502_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >3502_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_3502_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3502_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/3502_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3502_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57719 lines in total Total number of methylation call strings processed: 115438 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1914887 Total methylated C's in CpG context: 28773 Total methylated C's in CHG context: 3084 Total methylated C's in CHH context: 12967 Total C to T conversions in CpG context: 199776 Total C to T conversions in CHG context: 310413 Total C to T conversions in CHH context: 1359874 C methylated in CpG context: 12.6% C methylated in CHG context: 1.0% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_3502_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_3502_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_3502_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_3502_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_3502_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_3502_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_3502_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 3502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_3502_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_3502_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 3502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 3502_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 3502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_3502_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_3502_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_3502_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_3502_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 3502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 3502_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>3503_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >3503_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_3503_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 Now reading in Bismark result file 3503_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/3503_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/3503_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54898 lines in total Total number of methylation call strings processed: 109796 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1846095 Total methylated C's in CpG context: 29111 Total methylated C's in CHG context: 2883 Total methylated C's in CHH context: 12836 Total C to T conversions in CpG context: 190000 Total C to T conversions in CHG context: 297786 Total C to T conversions in CHH context: 1313479 C methylated in CpG context: 13.3% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_3503_R1_bismark_bt2_pe.deduplicated.txt was empty -> deleted CpG_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_3503_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_3503_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_3503_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_3503_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_3503_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_3503_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_3503_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_3503_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_3503_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 3503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_3503_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_3503_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 3503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 3503_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 3503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_3503_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_3503_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_3503_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 3503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 3503_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5201_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5201_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_5201_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5201_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5201_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5201_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: '5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57823 lines in total Total number of methylation call strings processed: 115646 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1739031 Total methylated C's in CpG context: 25095 Total methylated C's in CHG context: 2450 Total methylated C's in CHH context: 10982 Total C to T conversions in CpG context: 178413 Total C to T conversions in CHG context: 273483 Total C to T conversions in CHH context: 1248608 C methylated in CpG context: 12.3% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5201_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5201_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_5201_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_5201_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_5201_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_5201_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_5201_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5201_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_5201_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_5201_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5201_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5201_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 5201_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5201_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5201_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5201_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5201_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5201_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5201_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5202_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5202_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_5202_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5202_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5202_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5202_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57943 lines in total Total number of methylation call strings processed: 115886 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1975314 Total methylated C's in CpG context: 28144 Total methylated C's in CHG context: 3074 Total methylated C's in CHH context: 13166 Total C to T conversions in CpG context: 210593 Total C to T conversions in CHG context: 323279 Total C to T conversions in CHH context: 1397058 C methylated in CpG context: 11.8% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5202_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5202_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_5202_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_5202_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_5202_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_5202_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_5202_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5202_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_5202_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_5202_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5202_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5202_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 5202_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5202_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5202_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5202_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5202_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5202_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5202_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5203_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5203_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_5203_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5203_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5203_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5203_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: '5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 55643 lines in total Total number of methylation call strings processed: 111286 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1813834 Total methylated C's in CpG context: 29295 Total methylated C's in CHG context: 3166 Total methylated C's in CHH context: 14301 Total C to T conversions in CpG context: 186579 Total C to T conversions in CHG context: 290961 Total C to T conversions in CHH context: 1289532 C methylated in CpG context: 13.6% C methylated in CHG context: 1.1% C methylated in CHH context: 1.1% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5203_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5203_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_5203_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_5203_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_5203_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_5203_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_5203_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5203_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_5203_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_5203_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5203_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5203_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 5203_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5203_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5203_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5203_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5203_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5203_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5203_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5901_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5901_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_5901_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5901_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5901_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5901_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56513 lines in total Total number of methylation call strings processed: 113026 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1891864 Total methylated C's in CpG context: 30700 Total methylated C's in CHG context: 3083 Total methylated C's in CHH context: 13000 Total C to T conversions in CpG context: 199778 Total C to T conversions in CHG context: 309087 Total C to T conversions in CHH context: 1336216 C methylated in CpG context: 13.3% C methylated in CHG context: 1.0% C methylated in CHH context: 1.0% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5901_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5901_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_5901_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_5901_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_5901_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_5901_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_5901_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5901_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_5901_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_5901_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5901_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5901_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 5901_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5901_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5901_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5901_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5901_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5901_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5901_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5902_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5902_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_5902_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5902_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5902_R2.fq.gz" Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5902_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57479 lines in total Total number of methylation call strings processed: 114958 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1978606 Total methylated C's in CpG context: 28775 Total methylated C's in CHG context: 3057 Total methylated C's in CHH context: 13217 Total C to T conversions in CpG context: 207515 Total C to T conversions in CHG context: 321019 Total C to T conversions in CHH context: 1405023 C methylated in CpG context: 12.2% C methylated in CHG context: 0.9% C methylated in CHH context: 0.9% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5902_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5902_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_5902_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_5902_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_5902_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_5902_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_5902_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5902_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_5902_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_5902_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5902_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5902_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 5902_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5902_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5902_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5902_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5902_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5902_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5902_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>5903_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >5903_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_5903_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/5903_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/5903_R2.fq.gz" Now reading in Bismark result file 5903_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: '5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57076 lines in total Total number of methylation call strings processed: 114152 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1980266 Total methylated C's in CpG context: 29502 Total methylated C's in CHG context: 4260 Total methylated C's in CHH context: 18399 Total C to T conversions in CpG context: 213177 Total C to T conversions in CHG context: 323900 Total C to T conversions in CHH context: 1391028 C methylated in CpG context: 12.2% C methylated in CHG context: 1.3% C methylated in CHH context: 1.3% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 140 Maximum read length of Read 2: 140 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_5903_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_5903_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_5903_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_5903_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_5903_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_5903_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_5903_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: 5903_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_5903_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_5903_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: 5903_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: 5903_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file 5903_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_5903_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_5903_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_5903_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_5903_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file 5903_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file 5903_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_10_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_10_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_10_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_10_R2.fq.gz" Now reading in Bismark result file zr3534_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 55456 lines in total Total number of methylation call strings processed: 110912 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1340768 Total methylated C's in CpG context: 17015 Total methylated C's in CHG context: 1048 Total methylated C's in CHH context: 4335 Total C to T conversions in CpG context: 157144 Total C to T conversions in CHG context: 232950 Total C to T conversions in CHH context: 928276 C methylated in CpG context: 9.8% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_10_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_1_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_1_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_1_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54892 lines in total Total number of methylation call strings processed: 109784 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1330789 Total methylated C's in CpG context: 17210 Total methylated C's in CHG context: 1071 Total methylated C's in CHH context: 4667 Total C to T conversions in CpG context: 154648 Total C to T conversions in CHG context: 229591 Total C to T conversions in CHH context: 923602 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_2_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_2_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_2_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_2_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_2_R2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54949 lines in total Total number of methylation call strings processed: 109898 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1337084 Total methylated C's in CpG context: 16934 Total methylated C's in CHG context: 1053 Total methylated C's in CHH context: 4861 Total C to T conversions in CpG context: 156596 Total C to T conversions in CHG context: 230643 Total C to T conversions in CHH context: 926997 C methylated in CpG context: 9.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_2_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_3_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_3_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_3_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_3_R2.fq.gz" Now reading in Bismark result file zr3534_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54955 lines in total Total number of methylation call strings processed: 109910 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1361137 Total methylated C's in CpG context: 20085 Total methylated C's in CHG context: 1230 Total methylated C's in CHH context: 5181 Total C to T conversions in CpG context: 153239 Total C to T conversions in CHG context: 233513 Total C to T conversions in CHH context: 947889 C methylated in CpG context: 11.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_3_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_4_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_4_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 Now reading in Bismark result file zr3534_4_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_4_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_4_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 55259 lines in total Total number of methylation call strings processed: 110518 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1334307 Total methylated C's in CpG context: 18547 Total methylated C's in CHG context: 1068 Total methylated C's in CHH context: 4983 Total C to T conversions in CpG context: 153522 Total C to T conversions in CHG context: 230168 Total C to T conversions in CHH context: 926019 C methylated in CpG context: 10.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_4_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_5_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_5_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_5_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_5_R2.fq.gz" Now reading in Bismark result file zr3534_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 55086 lines in total Total number of methylation call strings processed: 110172 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1321450 Total methylated C's in CpG context: 18706 Total methylated C's in CHG context: 1142 Total methylated C's in CHH context: 4868 Total C to T conversions in CpG context: 149852 Total C to T conversions in CHG context: 227304 Total C to T conversions in CHH context: 919578 C methylated in CpG context: 11.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_5_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_6_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_6_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_6_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_6_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Merging individual splitting reports into overall report: 'zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54560 lines in total Total number of methylation call strings processed: 109120 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1329087 Total methylated C's in CpG context: 17277 Total methylated C's in CHG context: 1077 Total methylated C's in CHH context: 4605 Total C to T conversions in CpG context: 152699 Total C to T conversions in CHG context: 227992 Total C to T conversions in CHH context: 925437 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_6_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_7_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_7_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_7_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_7_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 55478 lines in total Total number of methylation call strings processed: 110956 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1350779 Total methylated C's in CpG context: 17175 Total methylated C's in CHG context: 1062 Total methylated C's in CHH context: 5015 Total C to T conversions in CpG context: 153801 Total C to T conversions in CHG context: 231013 Total C to T conversions in CHH context: 942713 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_7_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_8_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_8_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_8_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_8_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54631 lines in total Total number of methylation call strings processed: 109262 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1286222 Total methylated C's in CpG context: 16614 Total methylated C's in CHG context: 991 Total methylated C's in CHH context: 4536 Total C to T conversions in CpG context: 147209 Total C to T conversions in CHG context: 220589 Total C to T conversions in CHH context: 896283 C methylated in CpG context: 10.1% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_8_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3534_9_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3534_9_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3534_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3534_9_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3534_9_R2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 55727 lines in total Total number of methylation call strings processed: 111454 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1352824 Total methylated C's in CpG context: 17147 Total methylated C's in CHG context: 1109 Total methylated C's in CHH context: 4655 Total C to T conversions in CpG context: 158036 Total C to T conversions in CHG context: 235705 Total C to T conversions in CHH context: 936172 C methylated in CpG context: 9.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3534_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3534_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3534_9_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3534_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3534_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3534_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3534_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_10_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_10_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_10_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_10_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57147 lines in total Total number of methylation call strings processed: 114294 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1367044 Total methylated C's in CpG context: 18292 Total methylated C's in CHG context: 1099 Total methylated C's in CHH context: 4850 Total C to T conversions in CpG context: 158774 Total C to T conversions in CHG context: 236251 Total C to T conversions in CHH context: 947778 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_10_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_11_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_11_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 Warning: unable to close filehandle IN properly. skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_11_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_11_R2.fq.gz" Now reading in Bismark result file zr3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56886 lines in total Total number of methylation call strings processed: 113772 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1358219 Total methylated C's in CpG context: 17603 Total methylated C's in CHG context: 1113 Total methylated C's in CHH context: 5036 Total C to T conversions in CpG context: 157564 Total C to T conversions in CHG context: 234678 Total C to T conversions in CHH context: 942225 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_11_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_11_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_12_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_12_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_12_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_12_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57478 lines in total Total number of methylation call strings processed: 114956 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1353399 Total methylated C's in CpG context: 16221 Total methylated C's in CHG context: 1001 Total methylated C's in CHH context: 4482 Total C to T conversions in CpG context: 152373 Total C to T conversions in CHG context: 225562 Total C to T conversions in CHH context: 953760 C methylated in CpG context: 9.6% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_12_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_12_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_13_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_13_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_13_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_13_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57342 lines in total Total number of methylation call strings processed: 114684 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1406264 Total methylated C's in CpG context: 18175 Total methylated C's in CHG context: 1149 Total methylated C's in CHH context: 5038 Total C to T conversions in CpG context: 160953 Total C to T conversions in CHG context: 241126 Total C to T conversions in CHH context: 979823 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_13_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_13_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_14_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_14_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_14_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_14_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 58034 lines in total Total number of methylation call strings processed: 116068 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1392769 Total methylated C's in CpG context: 20439 Total methylated C's in CHG context: 1189 Total methylated C's in CHH context: 4943 Total C to T conversions in CpG context: 156912 Total C to T conversions in CHG context: 238595 Total C to T conversions in CHH context: 970691 C methylated in CpG context: 11.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_14_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_14_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_15_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_15_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_15_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_15_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57436 lines in total Total number of methylation call strings processed: 114872 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1385235 Total methylated C's in CpG context: 19228 Total methylated C's in CHG context: 1169 Total methylated C's in CHH context: 4747 Total C to T conversions in CpG context: 157318 Total C to T conversions in CHG context: 237701 Total C to T conversions in CHH context: 965072 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_15_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_15_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_16_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_16_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_16_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_16_R2.fq.gz" Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57429 lines in total Total number of methylation call strings processed: 114858 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1314284 Total methylated C's in CpG context: 17404 Total methylated C's in CHG context: 1122 Total methylated C's in CHH context: 4762 Total C to T conversions in CpG context: 152417 Total C to T conversions in CHG context: 227151 Total C to T conversions in CHH context: 911428 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_16_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_16_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_17_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_17_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_17_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_17_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57402 lines in total Total number of methylation call strings processed: 114804 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1379883 Total methylated C's in CpG context: 18203 Total methylated C's in CHG context: 1177 Total methylated C's in CHH context: 4744 Total C to T conversions in CpG context: 162900 Total C to T conversions in CHG context: 239940 Total C to T conversions in CHH context: 952919 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_17_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_17_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_18_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_18_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_18_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_18_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 58506 lines in total Total number of methylation call strings processed: 117012 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1400104 Total methylated C's in CpG context: 18495 Total methylated C's in CHG context: 1162 Total methylated C's in CHH context: 4926 Total C to T conversions in CpG context: 162988 Total C to T conversions in CHG context: 242924 Total C to T conversions in CHH context: 969609 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_18_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_18_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_19_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_19_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 Now reading in Bismark result file zr3644_19_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_19_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_19_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57782 lines in total Total number of methylation call strings processed: 115564 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1391498 Total methylated C's in CpG context: 17611 Total methylated C's in CHG context: 1159 Total methylated C's in CHH context: 5021 Total C to T conversions in CpG context: 160205 Total C to T conversions in CHG context: 239409 Total C to T conversions in CHH context: 968093 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_19_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_19_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_1_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_1_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_1_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 58412 lines in total Total number of methylation call strings processed: 116824 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1373705 Total methylated C's in CpG context: 16457 Total methylated C's in CHG context: 1093 Total methylated C's in CHH context: 4561 Total C to T conversions in CpG context: 160479 Total C to T conversions in CHG context: 238266 Total C to T conversions in CHH context: 952849 C methylated in CpG context: 9.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_20_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_20_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_20_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_20_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57403 lines in total Total number of methylation call strings processed: 114806 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1402572 Total methylated C's in CpG context: 17549 Total methylated C's in CHG context: 1151 Total methylated C's in CHH context: 5152 Total C to T conversions in CpG context: 162343 Total C to T conversions in CHG context: 241099 Total C to T conversions in CHH context: 975278 C methylated in CpG context: 9.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_20_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_20_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_21_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_21_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_21_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_21_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57158 lines in total Total number of methylation call strings processed: 114316 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1396963 Total methylated C's in CpG context: 18229 Total methylated C's in CHG context: 1108 Total methylated C's in CHH context: 4713 Total C to T conversions in CpG context: 160395 Total C to T conversions in CHG context: 240305 Total C to T conversions in CHH context: 972213 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_21_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_21_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_22_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_22_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_22_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_22_R2.fq.gz" Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57790 lines in total Total number of methylation call strings processed: 115580 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1400184 Total methylated C's in CpG context: 17967 Total methylated C's in CHG context: 1195 Total methylated C's in CHH context: 4901 Total C to T conversions in CpG context: 162565 Total C to T conversions in CHG context: 241491 Total C to T conversions in CHH context: 972065 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_22_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_22_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_23_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_23_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_23_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_23_R2.fq.gz" Now reading in Bismark result file zr3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57209 lines in total Total number of methylation call strings processed: 114418 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1354323 Total methylated C's in CpG context: 17488 Total methylated C's in CHG context: 1183 Total methylated C's in CHH context: 4909 Total C to T conversions in CpG context: 157505 Total C to T conversions in CHG context: 233818 Total C to T conversions in CHH context: 939420 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_23_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_23_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_24_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_24_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_24_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_24_R2.fq.gz" Now reading in Bismark result file zr3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 58133 lines in total Total number of methylation call strings processed: 116266 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1405268 Total methylated C's in CpG context: 18046 Total methylated C's in CHG context: 1163 Total methylated C's in CHH context: 4781 Total C to T conversions in CpG context: 163678 Total C to T conversions in CHG context: 242659 Total C to T conversions in CHH context: 974941 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_24_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_24_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_2_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_2_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_2_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_2_R2.fq.gz" Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56894 lines in total Total number of methylation call strings processed: 113788 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1418146 Total methylated C's in CpG context: 18079 Total methylated C's in CHG context: 1195 Total methylated C's in CHH context: 4889 Total C to T conversions in CpG context: 163292 Total C to T conversions in CHG context: 242611 Total C to T conversions in CHH context: 988080 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_2_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_3_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_3_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_3_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_3_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57491 lines in total Total number of methylation call strings processed: 114982 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1386996 Total methylated C's in CpG context: 17858 Total methylated C's in CHG context: 1119 Total methylated C's in CHH context: 4720 Total C to T conversions in CpG context: 160089 Total C to T conversions in CHG context: 237922 Total C to T conversions in CHH context: 965288 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_3_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_4_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_4_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_4_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_4_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57089 lines in total Total number of methylation call strings processed: 114178 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1371032 Total methylated C's in CpG context: 17454 Total methylated C's in CHG context: 1054 Total methylated C's in CHH context: 4473 Total C to T conversions in CpG context: 155258 Total C to T conversions in CHG context: 232556 Total C to T conversions in CHH context: 960237 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_4_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_5_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_5_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_5_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_5_R2.fq.gz" Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57597 lines in total Total number of methylation call strings processed: 115194 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1398234 Total methylated C's in CpG context: 17568 Total methylated C's in CHG context: 1182 Total methylated C's in CHH context: 5075 Total C to T conversions in CpG context: 159880 Total C to T conversions in CHG context: 239225 Total C to T conversions in CHH context: 975304 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_5_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_6_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_6_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_6_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_6_R2.fq.gz" Now reading in Bismark result file zr3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57974 lines in total Total number of methylation call strings processed: 115948 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1393231 Total methylated C's in CpG context: 17907 Total methylated C's in CHG context: 1145 Total methylated C's in CHH context: 4957 Total C to T conversions in CpG context: 159814 Total C to T conversions in CHG context: 237802 Total C to T conversions in CHH context: 971606 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_6_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_7_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_7_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 Now reading in Bismark result file zr3644_7_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_7_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_7_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57111 lines in total Total number of methylation call strings processed: 114222 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1384445 Total methylated C's in CpG context: 18084 Total methylated C's in CHG context: 1133 Total methylated C's in CHH context: 4741 Total C to T conversions in CpG context: 158018 Total C to T conversions in CHG context: 236329 Total C to T conversions in CHH context: 966140 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_7_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_8_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_8_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_8_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_8_R2.fq.gz" Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57359 lines in total Total number of methylation call strings processed: 114718 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1371764 Total methylated C's in CpG context: 17946 Total methylated C's in CHG context: 1112 Total methylated C's in CHH context: 5133 Total C to T conversions in CpG context: 158229 Total C to T conversions in CHG context: 236164 Total C to T conversions in CHH context: 953180 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_8_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zr3644_9_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zr3644_9_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zr3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zr3644_9_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zr3644_9_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56719 lines in total Total number of methylation call strings processed: 113438 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1283697 Total methylated C's in CpG context: 17534 Total methylated C's in CHG context: 1072 Total methylated C's in CHH context: 4784 Total C to T conversions in CpG context: 147837 Total C to T conversions in CHG context: 221612 Total C to T conversions in CHH context: 890858 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zr3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zr3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zr3644_9_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zr3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zr3644_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zr3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zr3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_1_R2.fq.gz" Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54267 lines in total Total number of methylation call strings processed: 108534 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1111357 Total methylated C's in CpG context: 16063 Total methylated C's in CHG context: 1008 Total methylated C's in CHH context: 4642 Total C to T conversions in CpG context: 135628 Total C to T conversions in CHG context: 198837 Total C to T conversions in CHH context: 755179 C methylated in CpG context: 10.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3616_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3616_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 Now reading in Bismark result file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_2_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54090 lines in total Total number of methylation call strings processed: 108180 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1094017 Total methylated C's in CpG context: 15537 Total methylated C's in CHG context: 972 Total methylated C's in CHH context: 4051 Total C to T conversions in CpG context: 133072 Total C to T conversions in CHG context: 195204 Total C to T conversions in CHH context: 745181 C methylated in CpG context: 10.5% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3616_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3616_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_3_R2.fq.gz" Now reading in Bismark result file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 53738 lines in total Total number of methylation call strings processed: 107476 Final Cytosine Methylation Report ================================= Total number of C's analysed: 999365 Total methylated C's in CpG context: 14715 Total methylated C's in CHG context: 901 Total methylated C's in CHH context: 3908 Total C to T conversions in CpG context: 119091 Total C to T conversions in CHG context: 177915 Total C to T conversions in CHH context: 682835 C methylated in CpG context: 11.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3616_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3616_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_4_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 53932 lines in total Total number of methylation call strings processed: 107864 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1054411 Total methylated C's in CpG context: 15340 Total methylated C's in CHG context: 965 Total methylated C's in CHH context: 4152 Total C to T conversions in CpG context: 127416 Total C to T conversions in CHG context: 189571 Total C to T conversions in CHH context: 716967 C methylated in CpG context: 10.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3616_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3616_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_5_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 54309 lines in total Total number of methylation call strings processed: 108618 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1037483 Total methylated C's in CpG context: 14188 Total methylated C's in CHG context: 898 Total methylated C's in CHH context: 4269 Total C to T conversions in CpG context: 125402 Total C to T conversions in CHG context: 185487 Total C to T conversions in CHH context: 707239 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3616_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3616_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_6_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 52888 lines in total Total number of methylation call strings processed: 105776 Final Cytosine Methylation Report ================================= Total number of C's analysed: 978778 Total methylated C's in CpG context: 13835 Total methylated C's in CHG context: 837 Total methylated C's in CHH context: 3682 Total C to T conversions in CpG context: 118881 Total C to T conversions in CHG context: 175160 Total C to T conversions in CHH context: 666383 C methylated in CpG context: 10.4% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3616_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3616_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_7_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 53945 lines in total Total number of methylation call strings processed: 107890 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1042333 Total methylated C's in CpG context: 15524 Total methylated C's in CHG context: 930 Total methylated C's in CHH context: 4069 Total C to T conversions in CpG context: 123948 Total C to T conversions in CHG context: 184748 Total C to T conversions in CHH context: 713114 C methylated in CpG context: 11.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3616_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3616_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 Now reading in Bismark result file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3616_8_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 53992 lines in total Total number of methylation call strings processed: 107984 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1057836 Total methylated C's in CpG context: 15560 Total methylated C's in CHG context: 953 Total methylated C's in CHH context: 4356 Total C to T conversions in CpG context: 128008 Total C to T conversions in CHG context: 189631 Total C to T conversions in CHH context: 719328 C methylated in CpG context: 10.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.6% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3616_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3616_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_10_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56946 lines in total Total number of methylation call strings processed: 113892 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1371132 Total methylated C's in CpG context: 18394 Total methylated C's in CHG context: 1125 Total methylated C's in CHH context: 4852 Total C to T conversions in CpG context: 159797 Total C to T conversions in CHG context: 237123 Total C to T conversions in CHH context: 949841 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_10_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_10_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_11_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56685 lines in total Total number of methylation call strings processed: 113370 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1361369 Total methylated C's in CpG context: 17748 Total methylated C's in CHG context: 1093 Total methylated C's in CHH context: 4739 Total C to T conversions in CpG context: 158161 Total C to T conversions in CHG context: 235802 Total C to T conversions in CHH context: 943826 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_11_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_11_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_12_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57357 lines in total Total number of methylation call strings processed: 114714 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1359316 Total methylated C's in CpG context: 16319 Total methylated C's in CHG context: 1018 Total methylated C's in CHH context: 4474 Total C to T conversions in CpG context: 153209 Total C to T conversions in CHG context: 226939 Total C to T conversions in CHH context: 957357 C methylated in CpG context: 9.6% C methylated in CHG context: 0.4% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_12_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_12_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_13_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57093 lines in total Total number of methylation call strings processed: 114186 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1407110 Total methylated C's in CpG context: 18235 Total methylated C's in CHG context: 1159 Total methylated C's in CHH context: 4777 Total C to T conversions in CpG context: 161556 Total C to T conversions in CHG context: 241902 Total C to T conversions in CHH context: 979481 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_13_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_13_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_14_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57792 lines in total Total number of methylation call strings processed: 115584 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1394909 Total methylated C's in CpG context: 20582 Total methylated C's in CHG context: 1188 Total methylated C's in CHH context: 4964 Total C to T conversions in CpG context: 157518 Total C to T conversions in CHG context: 239212 Total C to T conversions in CHH context: 971445 C methylated in CpG context: 11.6% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_14_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_14_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_15_R2.fq.gz" Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57288 lines in total Total number of methylation call strings processed: 114576 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1389611 Total methylated C's in CpG context: 19351 Total methylated C's in CHG context: 1181 Total methylated C's in CHH context: 4711 Total C to T conversions in CpG context: 158139 Total C to T conversions in CHG context: 238682 Total C to T conversions in CHH context: 967547 C methylated in CpG context: 10.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_15_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_15_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_16_R2.fq.gz" Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57099 lines in total Total number of methylation call strings processed: 114198 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1317943 Total methylated C's in CpG context: 17557 Total methylated C's in CHG context: 1110 Total methylated C's in CHH context: 4582 Total C to T conversions in CpG context: 153340 Total C to T conversions in CHG context: 227936 Total C to T conversions in CHH context: 913418 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_16_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_16_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_17_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57253 lines in total Total number of methylation call strings processed: 114506 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1386305 Total methylated C's in CpG context: 18302 Total methylated C's in CHG context: 1206 Total methylated C's in CHH context: 4800 Total C to T conversions in CpG context: 164021 Total C to T conversions in CHG context: 241401 Total C to T conversions in CHH context: 956575 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_17_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_17_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_18_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 58310 lines in total Total number of methylation call strings processed: 116620 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1404454 Total methylated C's in CpG context: 18596 Total methylated C's in CHG context: 1178 Total methylated C's in CHH context: 4934 Total C to T conversions in CpG context: 163930 Total C to T conversions in CHG context: 244043 Total C to T conversions in CHH context: 971773 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_18_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_18_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_19_R2.fq.gz" Now reading in Bismark result file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57474 lines in total Total number of methylation call strings processed: 114948 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1391794 Total methylated C's in CpG context: 17618 Total methylated C's in CHG context: 1166 Total methylated C's in CHH context: 4835 Total C to T conversions in CpG context: 160667 Total C to T conversions in CHG context: 239818 Total C to T conversions in CHH context: 967690 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_19_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_19_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_1_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 58103 lines in total Total number of methylation call strings processed: 116206 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1376985 Total methylated C's in CpG context: 16501 Total methylated C's in CHG context: 1093 Total methylated C's in CHH context: 4349 Total C to T conversions in CpG context: 161661 Total C to T conversions in CHG context: 239101 Total C to T conversions in CHH context: 954280 C methylated in CpG context: 9.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_1_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_1_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_20_R2.fq.gz" Now reading in Bismark result file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57268 lines in total Total number of methylation call strings processed: 114536 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1406127 Total methylated C's in CpG context: 17661 Total methylated C's in CHG context: 1145 Total methylated C's in CHH context: 4861 Total C to T conversions in CpG context: 163291 Total C to T conversions in CHG context: 241742 Total C to T conversions in CHH context: 977427 C methylated in CpG context: 9.8% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_20_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_20_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_21_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56890 lines in total Total number of methylation call strings processed: 113780 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1398119 Total methylated C's in CpG context: 18258 Total methylated C's in CHG context: 1122 Total methylated C's in CHH context: 4630 Total C to T conversions in CpG context: 160954 Total C to T conversions in CHG context: 240595 Total C to T conversions in CHH context: 972560 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_21_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_21_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_22_R2.fq.gz" Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57621 lines in total Total number of methylation call strings processed: 115242 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1404024 Total methylated C's in CpG context: 18040 Total methylated C's in CHG context: 1193 Total methylated C's in CHH context: 4894 Total C to T conversions in CpG context: 163600 Total C to T conversions in CHG context: 242229 Total C to T conversions in CHH context: 974068 C methylated in CpG context: 9.9% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_22_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_22_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_23_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57018 lines in total Total number of methylation call strings processed: 114036 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1359016 Total methylated C's in CpG context: 17577 Total methylated C's in CHG context: 1190 Total methylated C's in CHH context: 4695 Total C to T conversions in CpG context: 158275 Total C to T conversions in CHG context: 234950 Total C to T conversions in CHH context: 942329 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_23_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_23_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_24_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57896 lines in total Total number of methylation call strings processed: 115792 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1408564 Total methylated C's in CpG context: 18158 Total methylated C's in CHG context: 1181 Total methylated C's in CHH context: 4648 Total C to T conversions in CpG context: 164256 Total C to T conversions in CHG context: 243584 Total C to T conversions in CHH context: 976737 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_24_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_24_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 Now reading in Bismark result file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_2_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56666 lines in total Total number of methylation call strings processed: 113332 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1419476 Total methylated C's in CpG context: 18105 Total methylated C's in CHG context: 1208 Total methylated C's in CHH context: 5066 Total C to T conversions in CpG context: 163850 Total C to T conversions in CHG context: 242924 Total C to T conversions in CHH context: 988323 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_2_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_2_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_3_R2.fq.gz" Now reading in Bismark result file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57222 lines in total Total number of methylation call strings processed: 114444 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1388599 Total methylated C's in CpG context: 17982 Total methylated C's in CHG context: 1129 Total methylated C's in CHH context: 4596 Total C to T conversions in CpG context: 160404 Total C to T conversions in CHG context: 238481 Total C to T conversions in CHH context: 966007 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_3_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_3_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_4_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56883 lines in total Total number of methylation call strings processed: 113766 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1373862 Total methylated C's in CpG context: 17554 Total methylated C's in CHG context: 1064 Total methylated C's in CHH context: 4411 Total C to T conversions in CpG context: 156232 Total C to T conversions in CHG context: 233363 Total C to T conversions in CHH context: 961238 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_4_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_4_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_5_R2.fq.gz" Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57320 lines in total Total number of methylation call strings processed: 114640 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1397855 Total methylated C's in CpG context: 17726 Total methylated C's in CHG context: 1184 Total methylated C's in CHH context: 4779 Total C to T conversions in CpG context: 159944 Total C to T conversions in CHG context: 239762 Total C to T conversions in CHH context: 974460 C methylated in CpG context: 10.0% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_5_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_5_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_6_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57662 lines in total Total number of methylation call strings processed: 115324 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1394445 Total methylated C's in CpG context: 18046 Total methylated C's in CHG context: 1139 Total methylated C's in CHH context: 4804 Total C to T conversions in CpG context: 160195 Total C to T conversions in CHG context: 238321 Total C to T conversions in CHH context: 971940 C methylated in CpG context: 10.1% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_6_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_6_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_7_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56845 lines in total Total number of methylation call strings processed: 113690 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1385784 Total methylated C's in CpG context: 18157 Total methylated C's in CHG context: 1148 Total methylated C's in CHH context: 4695 Total C to T conversions in CpG context: 158602 Total C to T conversions in CHG context: 236768 Total C to T conversions in CHH context: 966414 C methylated in CpG context: 10.3% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_7_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_7_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_8_R2.fq.gz" Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 57165 lines in total Total number of methylation call strings processed: 114330 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1375616 Total methylated C's in CpG context: 18119 Total methylated C's in CHG context: 1126 Total methylated C's in CHH context: 5002 Total C to T conversions in CpG context: 158953 Total C to T conversions in CHG context: 237093 Total C to T conversions in CHH context: 955323 C methylated in CpG context: 10.2% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_8_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_8_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Checking file >>zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam<< for signs of file truncation... Now testing Bismark result file >zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam< for positional sorting (which would be bad...) ...passed! Writing result file containing methylation information for C in CpG context from the original top strand to CpG_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original top strand to CpG_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the complementary to original bottom strand to CpG_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CpG context from the original bottom strand to CpG_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original top strand to CHG_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original top strand to CHG_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the complementary to original bottom strand to CHG_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHG context from the original bottom strand to CHG_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original top strand to CHH_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original top strand to CHH_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the complementary to original bottom strand to CHH_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing result file containing methylation information for C in CHH context from the original bottom strand to CHH_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. skipping SAM header line: @HD VN:1.0 SO:unsorted skipping SAM header line: @SQ SN:NC_047559.1 LN:55785328 skipping SAM header line: @SQ SN:NC_047560.1 LN:73222313 skipping SAM header line: @SQ SN:NC_047561.1 LN:58319100 skipping SAM header line: @SQ SN:NC_047562.1 LN:53127865 skipping SAM header line: @SQ SN:NC_047563.1 LN:73550375 skipping SAM header line: @SQ SN:NC_047564.1 LN:60151564 skipping SAM header line: @SQ SN:NC_047565.1 LN:62107823 skipping SAM header line: @SQ SN:NC_047566.1 LN:58462999 skipping SAM header line: @SQ SN:NC_047567.1 LN:37089910 skipping SAM header line: @SQ SN:NC_047568.1 LN:57541580 skipping SAM header line: @SQ SN:NW_022994773.1 LN:129571 skipping SAM header line: @SQ SN:NW_022994774.1 LN:1185781 skipping SAM header line: @SQ SN:NW_022994775.1 LN:128451 skipping SAM header line: @SQ SN:NW_022994776.1 LN:124569 skipping SAM header line: @SQ SN:NW_022994777.1 LN:123505 skipping SAM header line: @SQ SN:NW_022994778.1 LN:761972 skipping SAM header line: @SQ SN:NW_022994779.1 LN:111600 skipping SAM header line: @SQ SN:NW_022994780.1 LN:109880 skipping SAM header line: @SQ SN:NW_022994781.1 LN:109004 skipping SAM header line: @SQ SN:NW_022994782.1 LN:105193 skipping SAM header line: @SQ SN:NW_022994783.1 LN:103107 Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994784.1 LN:1334230 skipping SAM header line: @SQ SN:NW_022994785.1 LN:99559 skipping SAM header line: @SQ SN:NW_022994786.1 LN:93417 skipping SAM header line: @SQ SN:NW_022994787.1 LN:85616 skipping SAM header line: @SQ SN:NW_022994788.1 LN:84435 skipping SAM header line: @SQ SN:NW_022994789.1 LN:725421 skipping SAM header line: @SQ SN:NW_022994790.1 LN:78344 skipping SAM header line: @SQ SN:NW_022994791.1 LN:77172 skipping SAM header line: @SQ SN:NW_022994792.1 LN:66789 skipping SAM header line: @SQ SN:NW_022994793.1 LN:66084 skipping SAM header line: @SQ SN:NW_022994794.1 LN:699037 skipping SAM header line: @SQ SN:NW_022994795.1 LN:63125 skipping SAM header line: @SQ SN:NW_022994796.1 LN:62774 skipping SAM header line: @SQ SN:NW_022994797.1 LN:60186 skipping SAM header line: @SQ SN:NW_022994798.1 LN:59881 Warning: unable to close filehandle IN properly. skipping SAM header line: @SQ SN:NW_022994799.1 LN:680695 skipping SAM header line: @SQ SN:NW_022994800.1 LN:57426 skipping SAM header line: @SQ SN:NW_022994801.1 LN:56398 skipping SAM header line: @SQ SN:NW_022994802.1 LN:52255 skipping SAM header line: @SQ SN:NW_022994803.1 LN:47562 skipping SAM header line: @SQ SN:NW_022994804.1 LN:45312 skipping SAM header line: @SQ SN:NW_022994805.1 LN:654836 skipping SAM header line: @SQ SN:NW_022994806.1 LN:34204 skipping SAM header line: @SQ SN:NW_022994807.1 LN:33063 skipping SAM header line: @SQ SN:NW_022994808.1 LN:32339 skipping SAM header line: @SQ SN:NW_022994809.1 LN:621026 skipping SAM header line: @SQ SN:NW_022994810.1 LN:30983 skipping SAM header line: @SQ SN:NW_022994811.1 LN:28060 skipping SAM header line: @SQ SN:NW_022994812.1 LN:26205 skipping SAM header line: @SQ SN:NW_022994813.1 LN:609159 skipping SAM header line: @SQ SN:NW_022994814.1 LN:18830 skipping SAM header line: @SQ SN:NW_022994815.1 LN:549086 skipping SAM header line: @SQ SN:NW_022994816.1 LN:985078 skipping SAM header line: @SQ SN:NW_022994817.1 LN:2254 skipping SAM header line: @SQ SN:NW_022994818.1 LN:1361 skipping SAM header line: @SQ SN:NW_022994819.1 LN:734241 skipping SAM header line: @SQ SN:NW_022994820.1 LN:658371 skipping SAM header line: @SQ SN:NW_022994821.1 LN:546250 skipping SAM header line: @SQ SN:NW_022994822.1 LN:614137 skipping SAM header line: @SQ SN:NW_022994823.1 LN:196267 skipping SAM header line: @SQ SN:NW_022994824.1 LN:461872 skipping SAM header line: @SQ SN:NW_022994825.1 LN:345626 skipping SAM header line: @SQ SN:NW_022994826.1 LN:153136 skipping SAM header line: @SQ SN:NW_022994827.1 LN:85676 skipping SAM header line: @SQ SN:NW_022994828.1 LN:316174 skipping SAM header line: @SQ SN:NW_022994829.1 LN:476514 skipping SAM header line: @SQ SN:NW_022994830.1 LN:534456 skipping SAM header line: @SQ SN:NW_022994831.1 LN:527944 skipping SAM header line: @SQ SN:NW_022994832.1 LN:513312 skipping SAM header line: @SQ SN:NW_022994833.1 LN:507370 skipping SAM header line: @SQ SN:NW_022994834.1 LN:496827 skipping SAM header line: @SQ SN:NW_022994835.1 LN:482992 skipping SAM header line: @SQ SN:NW_022994836.1 LN:471557 skipping SAM header line: @SQ SN:NW_022994837.1 LN:686402 skipping SAM header line: @SQ SN:NW_022994838.1 LN:445523 skipping SAM header line: @SQ SN:NW_022994839.1 LN:505355 skipping SAM header line: @SQ SN:NW_022994840.1 LN:408464 skipping SAM header line: @SQ SN:NW_022994841.1 LN:392916 skipping SAM header line: @SQ SN:NW_022994842.1 LN:346530 skipping SAM header line: @SQ SN:NW_022994843.1 LN:346498 skipping SAM header line: @SQ SN:NW_022994844.1 LN:984115 skipping SAM header line: @SQ SN:NW_022994845.1 LN:334217 skipping SAM header line: @SQ SN:NW_022994846.1 LN:330898 skipping SAM header line: @SQ SN:NW_022994847.1 LN:310459 skipping SAM header line: @SQ SN:NW_022994848.1 LN:975996 skipping SAM header line: @SQ SN:NW_022994849.1 LN:299473 skipping SAM header line: @SQ SN:NW_022994850.1 LN:724080 skipping SAM header line: @SQ SN:NW_022994851.1 LN:284019 skipping SAM header line: @SQ SN:NW_022994852.1 LN:380988 skipping SAM header line: @SQ SN:NW_022994853.1 LN:271986 skipping SAM header line: @SQ SN:NW_022994854.1 LN:271335 skipping SAM header line: @SQ SN:NW_022994855.1 LN:270660 skipping SAM header line: @SQ SN:NW_022994856.1 LN:269814 skipping SAM header line: @SQ SN:NW_022994857.1 LN:255287 skipping SAM header line: @SQ SN:NW_022994858.1 LN:250265 skipping SAM header line: @SQ SN:NW_022994859.1 LN:249553 skipping SAM header line: @SQ SN:NW_022994860.1 LN:243901 skipping SAM header line: @SQ SN:NW_022994861.1 LN:243737 skipping SAM header line: @SQ SN:NW_022994862.1 LN:230837 skipping SAM header line: @SQ SN:NW_022994863.1 LN:896916 skipping SAM header line: @SQ SN:NW_022994864.1 LN:230075 skipping SAM header line: @SQ SN:NW_022994865.1 LN:3851109 skipping SAM header line: @SQ SN:NW_022994866.1 LN:222500 skipping SAM header line: @SQ SN:NW_022994867.1 LN:221461 skipping SAM header line: @SQ SN:NW_022994868.1 LN:214429 skipping SAM header line: @SQ SN:NW_022994869.1 LN:208222 skipping SAM header line: @SQ SN:NW_022994870.1 LN:984156 skipping SAM header line: @SQ SN:NW_022994871.1 LN:303113 skipping SAM header line: @SQ SN:NW_022994872.1 LN:195767 skipping SAM header line: @SQ SN:NW_022994873.1 LN:192086 skipping SAM header line: @SQ SN:NW_022994874.1 LN:189815 skipping SAM header line: @SQ SN:NW_022994875.1 LN:180076 skipping SAM header line: @SQ SN:NW_022994876.1 LN:178302 skipping SAM header line: @SQ SN:NW_022994877.1 LN:371905 skipping SAM header line: @SQ SN:NW_022994878.1 LN:173440 Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam skipping SAM header line: @SQ SN:NW_022994879.1 LN:171659 skipping SAM header line: @SQ SN:NW_022994880.1 LN:169219 skipping SAM header line: @SQ SN:NW_022994881.1 LN:520634 skipping SAM header line: @SQ SN:NW_022994882.1 LN:167015 skipping SAM header line: @SQ SN:NW_022994883.1 LN:166538 skipping SAM header line: @SQ SN:NW_022994884.1 LN:165345 skipping SAM header line: @SQ SN:NW_022994885.1 LN:161001 skipping SAM header line: @SQ SN:NW_022994886.1 LN:803096 skipping SAM header line: @SQ SN:NW_022994887.1 LN:153941 skipping SAM header line: @SQ SN:NW_022994888.1 LN:153236 skipping SAM header line: @SQ SN:NW_022994889.1 LN:151090 skipping SAM header line: @SQ SN:NW_022994890.1 LN:226113 skipping SAM header line: @SQ SN:NW_022994891.1 LN:142569 skipping SAM header line: @SQ SN:NW_022994892.1 LN:139519 skipping SAM header line: @SQ SN:NW_022994893.1 LN:137056 skipping SAM header line: @SQ SN:NW_022994894.1 LN:135750 skipping SAM header line: @SQ SN:NW_022994895.1 LN:800838 skipping SAM header line: @SQ SN:NW_022994896.1 LN:123475 skipping SAM header line: @SQ SN:NW_022994897.1 LN:543823 skipping SAM header line: @SQ SN:NW_022994898.1 LN:63957 skipping SAM header line: @SQ SN:NW_022994899.1 LN:135656 skipping SAM header line: @SQ SN:NW_022994900.1 LN:158606 skipping SAM header line: @SQ SN:NW_022994901.1 LN:138885 skipping SAM header line: @SQ SN:NW_022994902.1 LN:213710 skipping SAM header line: @SQ SN:NW_022994903.1 LN:31917 skipping SAM header line: @SQ SN:NW_022994904.1 LN:192304 skipping SAM header line: @SQ SN:NW_022994905.1 LN:122499 skipping SAM header line: @SQ SN:NW_022994906.1 LN:24192 skipping SAM header line: @SQ SN:NW_022994907.1 LN:80452 skipping SAM header line: @SQ SN:NW_022994908.1 LN:34710 skipping SAM header line: @SQ SN:NW_022994909.1 LN:80340 skipping SAM header line: @SQ SN:NW_022994910.1 LN:59023 skipping SAM header line: @SQ SN:NW_022994911.1 LN:90223 skipping SAM header line: @SQ SN:NW_022994912.1 LN:80828 skipping SAM header line: @SQ SN:NW_022994913.1 LN:18545 skipping SAM header line: @SQ SN:NW_022994914.1 LN:79317 skipping SAM header line: @SQ SN:NW_022994915.1 LN:76490 skipping SAM header line: @SQ SN:NW_022994916.1 LN:77779 skipping SAM header line: @SQ SN:NW_022994917.1 LN:39112 skipping SAM header line: @SQ SN:NW_022994918.1 LN:404750 skipping SAM header line: @SQ SN:NW_022994919.1 LN:196227 skipping SAM header line: @SQ SN:NW_022994920.1 LN:39174 skipping SAM header line: @SQ SN:NW_022994921.1 LN:323512 skipping SAM header line: @SQ SN:NW_022994922.1 LN:83186 skipping SAM header line: @SQ SN:NW_022994923.1 LN:61906 skipping SAM header line: @SQ SN:NW_022994924.1 LN:127844 skipping SAM header line: @SQ SN:NW_022994925.1 LN:61549 skipping SAM header line: @SQ SN:NW_022994926.1 LN:81940 skipping SAM header line: @SQ SN:NW_022994927.1 LN:162546 skipping SAM header line: @SQ SN:NW_022994928.1 LN:69385 skipping SAM header line: @SQ SN:NW_022994929.1 LN:46878 skipping SAM header line: @SQ SN:NW_022994930.1 LN:145484 skipping SAM header line: @SQ SN:NW_022994931.1 LN:118323 skipping SAM header line: @SQ SN:NW_022994932.1 LN:123881 skipping SAM header line: @SQ SN:NW_022994933.1 LN:29995 skipping SAM header line: @SQ SN:NW_022994934.1 LN:161585 skipping SAM header line: @SQ SN:NW_022994935.1 LN:43805 skipping SAM header line: @SQ SN:NW_022994936.1 LN:297039 skipping SAM header line: @SQ SN:NW_022994937.1 LN:490709 skipping SAM header line: @SQ SN:NW_022994938.1 LN:203969 skipping SAM header line: @SQ SN:NW_022994939.1 LN:324655 skipping SAM header line: @SQ SN:NW_022994940.1 LN:218172 skipping SAM header line: @SQ SN:NW_022994941.1 LN:19044 skipping SAM header line: @SQ SN:NW_022994942.1 LN:61061 skipping SAM header line: @SQ SN:NW_022994943.1 LN:289459 skipping SAM header line: @SQ SN:NW_022994944.1 LN:261312 skipping SAM header line: @SQ SN:NW_022994945.1 LN:625727 skipping SAM header line: @SQ SN:NW_022994946.1 LN:333635 skipping SAM header line: @SQ SN:NW_022994947.1 LN:135775 skipping SAM header line: @SQ SN:NW_022994948.1 LN:858184 skipping SAM header line: @SQ SN:NW_022994949.1 LN:121447 skipping SAM header line: @SQ SN:NW_022994950.1 LN:33519 skipping SAM header line: @SQ SN:NW_022994951.1 LN:187731 skipping SAM header line: @SQ SN:NW_022994952.1 LN:219001 skipping SAM header line: @SQ SN:NW_022994953.1 LN:45830 skipping SAM header line: @SQ SN:NW_022994954.1 LN:129811 skipping SAM header line: @SQ SN:NW_022994955.1 LN:365466 skipping SAM header line: @SQ SN:NW_022994956.1 LN:433943 skipping SAM header line: @SQ SN:NW_022994957.1 LN:201146 skipping SAM header line: @SQ SN:NW_022994958.1 LN:172809 skipping SAM header line: @SQ SN:NW_022994959.1 LN:64928 skipping SAM header line: @SQ SN:NW_022994960.1 LN:137501 skipping SAM header line: @SQ SN:NW_022994961.1 LN:155459 skipping SAM header line: @SQ SN:NW_022994962.1 LN:175997 skipping SAM header line: @SQ SN:NW_022994963.1 LN:286963 skipping SAM header line: @SQ SN:NW_022994964.1 LN:245988 skipping SAM header line: @SQ SN:NW_022994965.1 LN:30682 skipping SAM header line: @SQ SN:NW_022994966.1 LN:514743 skipping SAM header line: @SQ SN:NW_022994967.1 LN:56505 skipping SAM header line: @SQ SN:NW_022994968.1 LN:91994 skipping SAM header line: @SQ SN:NW_022994969.1 LN:256332 skipping SAM header line: @SQ SN:NW_022994970.1 LN:36429 skipping SAM header line: @SQ SN:NW_022994971.1 LN:30384 skipping SAM header line: @SQ SN:NW_022994972.1 LN:189740 skipping SAM header line: @SQ SN:NW_022994973.1 LN:66576 skipping SAM header line: @SQ SN:NW_022994974.1 LN:36592 skipping SAM header line: @SQ SN:NW_022994975.1 LN:74180 skipping SAM header line: @SQ SN:NW_022994976.1 LN:30109 skipping SAM header line: @SQ SN:NW_022994977.1 LN:141708 skipping SAM header line: @SQ SN:NW_022994978.1 LN:113692 skipping SAM header line: @SQ SN:NW_022994979.1 LN:83790 skipping SAM header line: @SQ SN:NW_022994980.1 LN:6557 skipping SAM header line: @SQ SN:NW_022994981.1 LN:62922 skipping SAM header line: @SQ SN:NW_022994982.1 LN:153818 skipping SAM header line: @SQ SN:NW_022994983.1 LN:79855 skipping SAM header line: @SQ SN:NW_022994984.1 LN:42847 skipping SAM header line: @SQ SN:NW_022994985.1 LN:190097 skipping SAM header line: @SQ SN:NW_022994986.1 LN:135148 skipping SAM header line: @SQ SN:NW_022994987.1 LN:316463 skipping SAM header line: @SQ SN:NW_022994988.1 LN:28442 skipping SAM header line: @SQ SN:NW_022994989.1 LN:147472 skipping SAM header line: @SQ SN:NW_022994990.1 LN:30511 skipping SAM header line: @SQ SN:NW_022994991.1 LN:237136 skipping SAM header line: @SQ SN:NW_022994992.1 LN:107548 skipping SAM header line: @SQ SN:NW_022994993.1 LN:225226 skipping SAM header line: @SQ SN:NW_022994994.1 LN:24264 skipping SAM header line: @SQ SN:NW_022994995.1 LN:63071 skipping SAM header line: @SQ SN:NW_022994996.1 LN:98197 skipping SAM header line: @SQ SN:NW_022994997.1 LN:297219 skipping SAM header line: @SQ SN:NW_022994998.1 LN:55042 skipping SAM header line: @SQ SN:NC_001276.1 LN:18224 skipping SAM header line: @PG ID:Bismark VN:v0.22.3 CL:"bismark --path_to_bowtie /gscratch/srlab/programs/bowtie2-2.3.4.1-linux-x86_64/ -genome /gscratch/srlab/sr320/data/Cgig-genome/roslin_M/ -u 100000 -p 4 -score_min L,0,-0.6 --non_directional -1 /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R1.fq.gz -2 /gscratch/srlab/sr320/data/cg-big/zrtg3644_9_R2.fq.gz" Warning: unable to close filehandle IN properly. Now reading in Bismark result file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bam Warning: unable to close filehandle IN properly. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Now waiting for all child processes to complete Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Finished processing child process. Exiting.. Merging individual splitting reports into overall report: 'zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt' Merging from these individual files: zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27 zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28 Processed 56393 lines in total Total number of methylation call strings processed: 112786 Final Cytosine Methylation Report ================================= Total number of C's analysed: 1289022 Total methylated C's in CpG context: 17731 Total methylated C's in CHG context: 1087 Total methylated C's in CHH context: 4608 Total C to T conversions in CpG context: 148754 Total C to T conversions in CHG context: 223139 Total C to T conversions in CHH context: 893703 C methylated in CpG context: 10.7% C methylated in CHG context: 0.5% C methylated in CHH context: 0.5% Merging individual M-bias reports into overall M-bias statistics from these 28 individual files: zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.1.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.2.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.3.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.4.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.5.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.6.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.7.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.8.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.9.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.10.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.11.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.12.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.13.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.14.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.15.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.16.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.17.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.18.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.19.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.20.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.21.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.22.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.23.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.24.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.25.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.26.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.27.mbias zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt.28.mbias Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Determining maximum read lengths for M-Bias plots Maximum read length of Read 1: 115 Maximum read length of Read 2: 115 Perl module GD::Graph::lines is not installed, skipping drawing M-bias plots (only writing out M-bias plot table) Deleting unused files ... CpG_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CpG_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHG_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept CHH_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt contains data -> kept Using these input files: CpG_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CpG_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CpG_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CHG_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CHG_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CHG_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CHH_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CHH_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt CHH_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Summary of parameters for bismark2bedGraph conversion: ====================================================== bedGraph output: zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz output directory: >< remove whitespaces: no CX context: no (CpG context only, default) No-header selected: no Sorting method: Unix sort-based (smaller memory footprint, but slower) Sort buffer size: 75% Coverage threshold: 1 ============================================================================= Methylation information will now be written into a bedGraph and coverage file ============================================================================= Using the following files as Input: /gscratch/scrubbed/sr320/060921-bigC/CpG_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt /gscratch/scrubbed/sr320/060921-bigC/CpG_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt Writing bedGraph to file: zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz Also writing out a coverage file including counts methylated and unmethylated residues to file: zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bismark.cov.gz The genome of interest was specified to contain gazillions of chromosomes or scaffolds. Merging all input files and sorting everything in memory instead of writing out individual chromosome files... Writing all merged methylation calls to temp file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished writing methylation calls from CpG_OT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOT_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_CTOB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Finished writing methylation calls from CpG_OB_zrtg3644_9_R1_bismark_bt2_pe.deduplicated.txt to merged temp file Sorting input file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged by positions (using -S of 75%) Successfully deleted the temporary input file zrtg3644_9_R1_bismark_bt2_pe.deduplicated.bedGraph.gz.methylation_calls.merged Finished BedGraph conversion ... Found 78 alignment reports in current directory. Now trying to figure out whether there are corresponding optional reports Writing Bismark HTML report to >> 0501_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 0501_R1_bismark_bt2_PE_report.txt < Processing alignment report 0501_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 0501_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 0501_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 0501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 0501_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 0501_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 0502_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 0502_R1_bismark_bt2_PE_report.txt < Processing alignment report 0502_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 0502_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 0502_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 0502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 0502_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 0502_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 0503_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 0503_R1_bismark_bt2_PE_report.txt < Processing alignment report 0503_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 0503_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 0503_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 0503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 0503_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 0503_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 3501_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 3501_R1_bismark_bt2_PE_report.txt < Processing alignment report 3501_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 3501_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 3501_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 3501_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 3501_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 3501_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 3502_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 3502_R1_bismark_bt2_PE_report.txt < Processing alignment report 3502_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 3502_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 3502_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 3502_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 3502_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 3502_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 3503_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 3503_R1_bismark_bt2_PE_report.txt < Processing alignment report 3503_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 3503_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 3503_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 3503_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 3503_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 3503_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5201_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5201_R1_bismark_bt2_PE_report.txt < Processing alignment report 5201_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5201_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5201_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5201_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5201_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5201_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5202_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5202_R1_bismark_bt2_PE_report.txt < Processing alignment report 5202_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5202_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5202_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5202_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5202_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5202_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5203_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5203_R1_bismark_bt2_PE_report.txt < Processing alignment report 5203_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5203_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5203_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5203_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5203_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5203_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5901_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5901_R1_bismark_bt2_PE_report.txt < Processing alignment report 5901_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5901_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5901_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5901_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5901_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5901_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5902_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5902_R1_bismark_bt2_PE_report.txt < Processing alignment report 5902_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5902_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5902_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5902_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5902_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5902_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> 5903_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > 5903_R1_bismark_bt2_PE_report.txt < Processing alignment report 5903_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > 5903_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report 5903_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report 5903_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > 5903_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report 5903_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_10_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_10_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_10_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_10_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_10_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_10_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_10_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_1_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_1_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_1_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_1_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_1_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_1_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_1_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_2_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_2_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_2_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_2_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_2_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_2_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_2_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_3_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_3_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_3_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_3_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_3_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_3_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_3_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_4_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_4_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_4_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_4_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_4_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_4_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_4_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_5_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_5_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_5_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_5_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_5_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_5_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_5_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_6_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_6_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_6_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_6_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_6_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_6_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_6_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_7_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_7_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_7_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_7_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_7_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_7_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_7_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_8_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_8_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_8_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_8_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_8_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_8_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_8_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3534_9_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3534_9_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3534_9_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3534_9_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3534_9_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3534_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3534_9_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3534_9_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_10_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_10_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_10_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_10_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_10_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_10_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_10_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_11_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_11_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_11_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_11_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_11_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_11_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_11_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_12_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_12_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_12_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_12_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_12_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_12_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_12_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_13_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_13_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_13_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_13_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_13_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_13_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_13_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_14_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_14_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_14_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_14_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_14_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_14_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_14_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_15_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_15_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_15_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_15_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_15_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_15_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_15_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_16_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_16_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_16_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_16_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_16_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_16_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_16_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_17_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_17_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_17_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_17_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_17_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_17_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_17_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_18_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_18_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_18_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_18_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_18_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_18_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_18_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_19_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_19_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_19_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_19_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_19_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_19_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_19_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_1_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_1_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_1_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_1_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_1_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_1_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_1_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_20_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_20_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_20_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_20_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_20_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_20_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_20_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_21_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_21_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_21_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_21_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_21_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_21_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_21_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_22_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_22_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_22_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_22_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_22_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_22_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_22_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_23_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_23_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_23_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_23_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_23_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_23_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_23_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_24_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_24_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_24_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_24_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_24_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_24_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_24_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_2_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_2_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_2_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_2_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_2_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_2_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_2_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_3_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_3_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_3_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_3_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_3_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_3_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_3_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_4_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_4_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_4_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_4_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_4_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_4_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_4_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_5_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_5_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_5_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_5_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_5_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_5_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_5_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_6_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_6_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_6_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_6_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_6_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_6_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_6_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_7_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_7_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_7_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_7_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_7_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_7_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_7_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_8_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_8_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_8_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_8_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_8_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_8_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_8_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zr3644_9_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zr3644_9_R1_bismark_bt2_PE_report.txt < Processing alignment report zr3644_9_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zr3644_9_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zr3644_9_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zr3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zr3644_9_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zr3644_9_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3616_1_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3616_1_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3616_1_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3616_1_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3616_1_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3616_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3616_1_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3616_1_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3616_2_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3616_2_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3616_2_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3616_2_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3616_2_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3616_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3616_2_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3616_2_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3616_3_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3616_3_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3616_3_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3616_3_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3616_3_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3616_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3616_3_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3616_3_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3616_4_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3616_4_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3616_4_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3616_4_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3616_4_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3616_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3616_4_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3616_4_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3616_5_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3616_5_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3616_5_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3616_5_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3616_5_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3616_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3616_5_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3616_5_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3616_6_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3616_6_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3616_6_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3616_6_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3616_6_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3616_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3616_6_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3616_6_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3616_7_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3616_7_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3616_7_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3616_7_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3616_7_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3616_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3616_7_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3616_7_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3616_8_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3616_8_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3616_8_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3616_8_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3616_8_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3616_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3616_8_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3616_8_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_10_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_10_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_10_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_10_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_10_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_10_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_10_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_10_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_11_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_11_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_11_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_11_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_11_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_11_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_11_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_11_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_12_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_12_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_12_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_12_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_12_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_12_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_12_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_12_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_13_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_13_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_13_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_13_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_13_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_13_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_13_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_13_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_14_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_14_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_14_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_14_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_14_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_14_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_14_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_14_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_15_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_15_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_15_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_15_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_15_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_15_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_15_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_15_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_16_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_16_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_16_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_16_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_16_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_16_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_16_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_16_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_17_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_17_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_17_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_17_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_17_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_17_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_17_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_17_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_18_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_18_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_18_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_18_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_18_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_18_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_18_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_18_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_19_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_19_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_19_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_19_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_19_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_19_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_19_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_19_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_1_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_1_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_1_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_1_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_1_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_1_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_1_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_1_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_20_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_20_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_20_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_20_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_20_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_20_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_20_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_20_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_21_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_21_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_21_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_21_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_21_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_21_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_21_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_21_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_22_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_22_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_22_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_22_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_22_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_22_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_22_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_22_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_23_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_23_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_23_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_23_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_23_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_23_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_23_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_23_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_24_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_24_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_24_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_24_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_24_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_24_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_24_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_24_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_2_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_2_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_2_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_2_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_2_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_2_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_2_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_2_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_3_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_3_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_3_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_3_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_3_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_3_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_3_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_3_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_4_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_4_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_4_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_4_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_4_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_4_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_4_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_4_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_5_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_5_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_5_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_5_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_5_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_5_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_5_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_5_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_6_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_6_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_6_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_6_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_6_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_6_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_6_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_6_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_7_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_7_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_7_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_7_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_7_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_7_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_7_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_7_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_8_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_8_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_8_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_8_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_8_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_8_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_8_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_8_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== Writing Bismark HTML report to >> zrtg3644_9_R1_bismark_bt2_PE_report.html << ============================================================================================================== Using the following alignment report: > zrtg3644_9_R1_bismark_bt2_PE_report.txt < Processing alignment report zrtg3644_9_R1_bismark_bt2_PE_report.txt ... Complete Using the following deduplication report: > zrtg3644_9_R1_bismark_bt2_pe.deduplication_report.txt < Processing deduplication report zrtg3644_9_R1_bismark_bt2_pe.deduplication_report.txt ... Complete Using the following splitting report: > zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt < Processing splitting report zrtg3644_9_R1_bismark_bt2_pe.deduplicated_splitting_report.txt ... Complete Using the following M-bias report: > zrtg3644_9_R1_bismark_bt2_pe.deduplicated.M-bias.txt < Processing M-bias report zrtg3644_9_R1_bismark_bt2_pe.deduplicated.M-bias.txt ... Complete No nucleotide coverage report file specified, skipping this step ============================================================================================================== No Bismark/Bowtie2 single-end BAM files detected Found Bismark/Bowtie2 paired-end files No Bismark/HISAT2 single-end BAM files detected No Bismark/HISAT2 paired-end BAM files detected Generating Bismark summary report from 78 Bismark BAM file(s)... >> Reading from Bismark report: 0501_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 0502_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 0503_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 3501_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 3502_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 3503_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5201_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5202_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5203_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5901_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5902_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: 5903_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_10_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_1_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_2_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_3_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_4_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_5_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_6_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_7_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_8_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3534_9_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_10_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_11_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_12_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_13_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_14_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_15_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_16_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_17_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_18_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_19_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_1_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_20_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_21_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_22_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_23_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_24_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_2_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_3_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_4_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_5_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_6_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_7_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_8_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zr3644_9_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3616_1_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3616_2_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3616_3_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3616_4_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3616_5_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3616_6_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3616_7_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3616_8_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_10_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_11_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_12_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_13_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_14_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_15_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_16_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_17_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_18_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_19_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_1_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_20_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_21_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_22_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_23_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_24_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_2_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_3_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_4_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_5_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_6_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_7_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_8_R1_bismark_bt2_PE_report.txt >> Reading from Bismark report: zrtg3644_9_R1_bismark_bt2_PE_report.txt Wrote Bismark project summary to >> bismark_summary_report.html << [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/sr320/060921-bigC [INFO ] bismark : Found 78 bismark alignment reports [INFO ] bismark : Found 78 bismark dedup reports [INFO ] bismark : Found 78 bismark methextract reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... [bam_sort_core] merging from 0 files and 28 in-memory blocks... 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